Variant rs8531 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017622.3(BORCS6):c.765A>C(p.Pro255Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 1,601,868 control chromosomes in the GnomAD database, including 507,586 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 0.73 ( 42214 hom., cov: 33)

Exomes 𝑓: 0.79 ( 465372 hom. )

Consequence

BORCS6
NM_017622.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

BORCS6 (HGNC:25939): (BLOC-1 related complex subunit 6) Enables identical protein binding activity. Involved in lysosome localization. Part of BORC complex. [provided by Alliance of Genome Resources, Apr 2022]

BORCS6 links:

ENSG00000279152 (HGNC:):

ENSG00000279152 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP7

Synonymous conserved (PhyloP=-0.049 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BORCS6	NM_017622.3 link	c.765A>C	p.Pro255Pro	synonymous_variant	1/1	ENST00000389017.6	NP_060092.2	Q96GS4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BORCS6	ENST00000389017.6 link	c.765A>C	p.Pro255Pro	synonymous_variant	1/1	6	NM_017622.3	ENSP00000373669.4		Q96GS4
ENSG00000279152	ENST00000622992.1 link	n.444T>G		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.733

AC:

111438

AN:

152004

Hom.:

42186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.789

Gnomad AMR

AF:

0.554

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.300

Gnomad SAS

AF:

0.783

Gnomad FIN

AF:

0.856

Gnomad MID

AF:

0.640

Gnomad NFE

AF:

0.829

Gnomad OTH

AF:

0.711

GnomAD3 exomes

AF:

0.707

AC:

161089

AN:

227730

Hom.:

61188

AF XY:

0.727

AC XY:

90223

AN XY:

124088

show subpopulations

Gnomad AFR exome

AF:

0.657

Gnomad AMR exome

AF:

0.400

Gnomad ASJ exome

AF:

0.629

Gnomad EAS exome

AF:

0.300

Gnomad SAS exome

AF:

0.796

Gnomad FIN exome

AF:

0.853

Gnomad NFE exome

AF:

0.830

Gnomad OTH exome

AF:

0.729

GnomAD4 exome

AF:

0.792

AC:

1148315

AN:

1449748

Hom.:

465372

Cov.:

AF XY:

0.794

AC XY:

571981

AN XY:

720474

show subpopulations

Gnomad4 AFR exome

AF:

0.655

Gnomad4 AMR exome

AF:

0.417

Gnomad4 ASJ exome

AF:

0.627

Gnomad4 EAS exome

AF:

0.288

Gnomad4 SAS exome

AF:

0.795

Gnomad4 FIN exome

AF:

0.858

Gnomad4 NFE exome

AF:

0.832

Gnomad4 OTH exome

AF:

0.751

GnomAD4 genome

AF:

0.733

AC:

111508

AN:

152120

Hom.:

42214

Cov.:

AF XY:

0.730

AC XY:

54263

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.669

Gnomad4 AMR

AF:

0.553

Gnomad4 ASJ

AF:

0.614

Gnomad4 EAS

AF:

0.299

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.856

Gnomad4 NFE

AF:

0.829

Gnomad4 OTH

AF:

0.704

Alfa

AF:

0.799

Hom.:

70911

Bravo

AF:

0.702

Asia WGS

AF:

0.573

AC:

1996

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over