Genetic Variant BORCS7:c.*897C>T (chr10-102863821-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001136200.2(BORCS7):c.*897C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,170 control chromosomes in the GnomAD database, including 3,542 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 0.21 ( 3542 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

BORCS7
NM_001136200.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00200

Publications

82 publications found

Variant links:

Genes affected

BORCS7 (HGNC:23516): (BLOC-1 related complex subunit 7) Part of BORC complex. [provided by Alliance of Genome Resources, Apr 2022]

BORCS7 links:

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:

ENSG00000296999 (HGNC:):

ENSG00000296999 links:

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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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136200.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BORCS7	NM_001136200.2	MANE Select	c.*897C>T	3_prime_UTR	Exon 5 of 5	NP_001129672.1	Q96B45
BORCS7	NM_144591.5		c.*100C>T	3_prime_UTR	Exon 6 of 6	NP_653192.2	Q96B45
BORCS7-ASMT	NR_037644.1		n.406+889C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BORCS7	ENST00000339834.10	TSL:1 MANE Select	c.*897C>T	3_prime_UTR	Exon 5 of 5	ENSP00000342331.5	Q96B45
BORCS7	ENST00000369883.3	TSL:1	c.*100C>T	3_prime_UTR	Exon 6 of 6	ENSP00000358899.3	Q96B45
BORCS7-ASMT	ENST00000299353.6	TSL:5	n.*8+889C>T	intron	N/A	ENSP00000299353.5

Frequencies

GnomAD3 genomes

AF:

0.210

AC:

31974

AN:

152050

Hom.:

3542

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.209

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.101

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.224

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

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)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.210

AC:

31977

AN:

152168

Hom.:

3542

Cov.:

AF XY:

0.207

AC XY:

15383

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.157

AC:

6505

AN:

41516

American (AMR)

AF:

0.209

AC:

3191

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

975

AN:

3470

East Asian (EAS)

AF:

0.160

AC:

828

AN:

5184

South Asian (SAS)

AF:

0.102

AC:

494

AN:

4822

European-Finnish (FIN)

AF:

0.209

AC:

2211

AN:

10600

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.251

AC:

17071

AN:

67994

Other (OTH)

AF:

0.223

AC:

471

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1308

2615

3923

5230

6538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.239

Hom.:

14704

Bravo

AF:

0.210

Asia WGS

AF:

0.121

AC:

419

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

-0.0020

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over