Variant 7-107615103-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018844.4(BCAP29):c.690+1671T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 407,354 control chromosomes in the GnomAD database, including 109,879 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 0.72 ( 39661 hom., cov: 32)

Exomes 𝑓: 0.74 ( 70218 hom. )

Consequence

BCAP29
NM_018844.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.150

Variant links:

Genes affected

BCAP29 (HGNC:24131): (B cell receptor associated protein 29) Involved in osteoblast differentiation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

BCAP29 links:

DUS4L-BCAP29 (HGNC:54422): (DUS4L-BCAP29 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring DUS4L (dihydrouridine synthase 4 like) and BCAP29 (B cell receptor associated protein 29) genes on chromosome 7. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2019]

DUS4L-BCAP29 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCAP29	NM_018844.4 link	c.690+1671T>C		intron_variant		ENST00000005259.9	NP_061332.2	Q9UHQ4-1E9PAJ1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAP29	ENST00000005259.9 link	c.690+1671T>C		intron_variant		1	NM_018844.4	ENSP00000005259.4		Q9UHQ4-1
DUS4L-BCAP29	ENST00000673757.1 link	c.1489+1371T>C		intron_variant				ENSP00000501026.1		A0A669KAY5

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

109690

AN:

151990

Hom.:

39641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.744

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.679

Gnomad EAS

AF:

0.670

Gnomad SAS

AF:

0.844

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.727

GnomAD4 exome

AF:

0.738

AC:

188496

AN:

255246

Hom.:

70218

AF XY:

0.746

AC XY:

106892

AN XY:

143244

show subpopulations

Gnomad4 AFR exome

AF:

0.744

Gnomad4 AMR exome

AF:

0.729

Gnomad4 ASJ exome

AF:

0.662

Gnomad4 EAS exome

AF:

0.677

Gnomad4 SAS exome

AF:

0.835

Gnomad4 FIN exome

AF:

0.727

Gnomad4 NFE exome

AF:

0.713

Gnomad4 OTH exome

AF:

0.724

GnomAD4 genome

AF:

0.722

AC:

109756

AN:

152108

Hom.:

39661

Cov.:

AF XY:

0.723

AC XY:

53739

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.744

Gnomad4 AMR

AF:

0.716

Gnomad4 ASJ

AF:

0.679

Gnomad4 EAS

AF:

0.669

Gnomad4 SAS

AF:

0.845

Gnomad4 FIN

AF:

0.717

Gnomad4 NFE

AF:

0.707

Gnomad4 OTH

AF:

0.726

Alfa

AF:

0.684

Hom.:

5857

Bravo

AF:

0.717

Asia WGS

AF:

0.743

AC:

2585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

DANN

Benign

0.73

Splicing

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