dbSNP rs1046778: BORCS7-ASMT:n.*2162T>C (chr10-102901727-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000299353.6(BORCS7-ASMT):n.*2162T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,140 control chromosomes in the GnomAD database, including 7,060 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.30 ( 7056 hom., cov: 31)

Exomes 𝑓: 0.26 ( 4 hom. )

Consequence

BORCS7-ASMT
ENST00000299353.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.280

Publications

55 publications found

Variant links:

Genes affected

BORCS7-ASMT (HGNC:49183): (BORCS7-ASMT readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C10orf32 (chromosome 10 open reading frame 32) and AS3MT (arsenic, +3 oxidation state, methyltransferase) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]

BORCS7-ASMT links:

AS3MT (HGNC:17452): (arsenite methyltransferase) AS3MT catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to trivalent arsenical and may play a role in arsenic metabolism (Lin et al., 2002 [PubMed 11790780]).[supplied by OMIM, Mar 2008]

AS3MT links:

ENSG00000286575 (HGNC:):

ENSG00000286575 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000299353.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
AS3MT	NM_020682.4	MANE Select	c.*1027T>C	3_prime_UTR	Exon 11 of 11	NP_065733.2
BORCS7-ASMT	NR_037644.1		n.2560T>C	non_coding_transcript_exon	Exon 15 of 15
LOC107984265	NR_160733.1		n.169-1217A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*2162T>C	non_coding_transcript_exon	Exon 15 of 15	ENSP00000299353.5
AS3MT	ENST00000369880.8	TSL:1 MANE Select	c.*1027T>C	3_prime_UTR	Exon 11 of 11	ENSP00000358896.3
BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*2162T>C	3_prime_UTR	Exon 15 of 15	ENSP00000299353.5

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45440

AN:

151952

Hom.:

7048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.256

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.470

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.257

AC:

AN:

Hom.:

Cov.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.167

AC:

AN:

East Asian (EAS)

AF:

0.417

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.300

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.211

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.440

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.299

AC:

45484

AN:

152070

Hom.:

7056

Cov.:

AF XY:

0.298

AC XY:

22117

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.257

AC:

10652

AN:

41480

American (AMR)

AF:

0.281

AC:

4285

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.314

AC:

1091

AN:

3472

East Asian (EAS)

AF:

0.470

AC:

2429

AN:

5170

South Asian (SAS)

AF:

0.358

AC:

1723

AN:

4816

European-Finnish (FIN)

AF:

0.294

AC:

3100

AN:

10558

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.313

AC:

21248

AN:

67984

Other (OTH)

AF:

0.313

AC:

660

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1603

3205

4808

6410

8013

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.304

Hom.:

22449

Bravo

AF:

0.295

Asia WGS

AF:

0.369

AC:

1280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.3

(source)

DANN

Benign

0.68

PhyloP100

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over