7-107617676-T-C

Variant names:

• chr7-107617676-T-C
• rs10273733
• NM_018844.4:c.691-652T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018844.4(BCAP29):​c.691-652T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 152,104 control chromosomes in the GnomAD database, including 43,337 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 0.75 (43337 hom., cov: 32)
• Consequence: BCAP29 NM_018844.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.624
• Publications: 11 publications found

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: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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAP29	NM_018844.4	c.691-652T>C		intron_variant	Intron 7 of 7	ENST00000005259.9	NP_061332.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAP29	ENST00000005259.9	c.691-652T>C		intron_variant	Intron 7 of 7	1	NM_018844.4	ENSP00000005259.4
DUS4L-BCAP29	ENST00000673665.1	c.1411-652T>C		intron_variant	Intron 12 of 12			ENSP00000501082.1

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114313 AN: 151986 Hom.: 43293 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.752 AC: 114411 AN: 152104 Hom.: 43337 Cov.: 32 AF XY: 0.752 AC XY: 55933 AN XY: 74340

African (AFR) AF: 0.847 AC: 35144 AN: 41512

American (AMR) AF: 0.728 AC: 11114 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2361 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3451 AN: 5164

South Asian (SAS) AF: 0.846 AC: 4081 AN: 4824

European-Finnish (FIN) AF: 0.719 AC: 7593 AN: 10564

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48232 AN: 67978

Other (OTH) AF: 0.751 AC: 1587 AN: 2112

Alfa AF: 0.722 Hom.: 61497

Bravo AF: 0.751

Asia WGS AF: 0.750 AC: 2606 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.44
PhyloP100		-0.62
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10273733; hg19: chr7-107258121;