NM_018844.4:c.589+3595C>T

Variant names:

• chr7-107604100-C-T
• rs10953541
• NM_018844.4:c.589+3595C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 82 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=-0.93).
• 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 rank	MANE	Protein	UniProt
BCAP29	NM_018844.4	c.589+3595C>T		intron_variant	Intron 6 of 7	ENST00000005259.9	NP_061332.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAP29	ENST00000005259.9	c.589+3595C>T		intron_variant	Intron 6 of 7	1	NM_018844.4	ENSP00000005259.4
DUS4L-BCAP29	ENST00000673665.1	c.1309+3595C>T		intron_variant	Intron 11 of 12			ENSP00000501082.1

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

African (AFR) AF: 0.0456 AC: 1889 AN: 41450

American (AMR) AF: 0.161 AC: 2453 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3470

East Asian (EAS) AF: 0.137 AC: 707 AN: 5166

South Asian (SAS) AF: 0.153 AC: 735 AN: 4808

European-Finnish (FIN) AF: 0.251 AC: 2640 AN: 10524

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16425 AN: 67962

Other (OTH) AF: 0.159 AC: 334 AN: 2106

Alfa AF: 0.219 Hom.: 12814

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
PhyloP100		0.068
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: rs10953541; hg19: chr7-107244545;