7-107617676-T-C

Position:

• chr7-107617676-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.95).
• 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/exons	MANE	UniProt
BCAP29	NM_018844.4	c.691-652T>C		intron_variant		ENST00000005259.9
DUS4L-BCAP29	NR_163940.2	n.1759-652T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAP29	ENST00000005259.9	c.691-652T>C		intron_variant		1	NM_018844.4	P1

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

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.751

Alfa AF: 0.713 Hom.: 37440

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10273733; hg19: chr7-107258121;