dbSNP rs7098825: BORCS7-ASMT:n.*9-1328T>C (chr10-102868477-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.*9-1328T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,116 control chromosomes in the GnomAD database, including 1,124 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 0.11 ( 1124 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

BORCS7-ASMT
ENST00000299353.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.612

Publications

20 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:

U6 (HGNC:):

U6 links:

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new If you want to explore the variant's impact on the transcript ENST00000299353.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BORCS7-ASMT	NR_037644.1		n.407-1328T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*9-1328T>C	intron	N/A	ENSP00000299353.5
U6	ENST00000636230.1	TSL:6	n.57T>C	non_coding_transcript_exon	Exon 1 of 1
ENSG00000296999	ENST00000744161.1		n.88-1844A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16690

AN:

151998

Hom.:

1117

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0815

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.0799

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.0951

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.117

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.110

AC:

16715

AN:

152116

Hom.:

1124

Cov.:

AF XY:

0.112

AC XY:

8298

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0816

AC:

3386

AN:

41484

American (AMR)

AF:

0.149

AC:

2268

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0799

AC:

277

AN:

3468

East Asian (EAS)

AF:

0.297

AC:

1536

AN:

5172

South Asian (SAS)

AF:

0.191

AC:

920

AN:

4818

European-Finnish (FIN)

AF:

0.0951

AC:

1007

AN:

10594

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.103

AC:

7018

AN:

67994

Other (OTH)

AF:

0.120

AC:

253

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

754

1508

2263

3017

3771

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.102

Hom.:

147

Bravo

AF:

0.113

Asia WGS

AF:

0.211

AC:

733

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.8

(source)

DANN

Benign

0.59

PhyloP100

-0.61

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over