rs10953541

Positions:

• chr7-107604100-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018844.4(BCAP29):​c.589+3595C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,956 control chromosomes in the GnomAD database, including 2,798 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 0.17 (2798 hom., cov: 30)
• Consequence: BCAP29 NM_018844.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680

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]

DUS4L-BCAP29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAP29	NM_018844.4	c.589+3595C>T		intron_variant		ENST00000005259.9
DUS4L-BCAP29	NR_163940.2	n.1578+3595C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAP29	ENST00000005259.9	c.589+3595C>T		intron_variant		1	NM_018844.4	P1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26057 AN: 151836 Hom.: 2800 Cov.: 30

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.159

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.171 AC: 26048 AN: 151956 Hom.: 2798 Cov.: 30 AF XY: 0.171 AC XY: 12662 AN XY: 74238

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.159

Alfa AF: 0.227 Hom.: 6202

Bravo AF: 0.160

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10953541; hg19: chr7-107244545;