Genetic Variant BCAP29:c.691-652T>C (chr7-107617676-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.624

Publications

11 publications found

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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new If you want to explore the variant's impact on the transcript NM_018844.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018844.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCAP29	NM_018844.4	MANE Select	c.691-652T>C	intron	N/A	NP_061332.2	E9PAJ1
DUS4L-BCAP29	NM_001371364.2		c.1490-652T>C	intron	N/A	NP_001358293.1	A0A669KAY5
DUS4L-BCAP29	NM_001371365.2		c.1411-652T>C	intron	N/A	NP_001358294.1	A0A669KB27

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BCAP29	ENST00000005259.9	TSL:1 MANE Select	c.691-652T>C	intron	N/A	ENSP00000005259.4	Q9UHQ4-1
DUS4L-BCAP29	ENST00000673665.1		c.1411-652T>C	intron	N/A	ENSP00000501082.1	A0A669KB27
DUS4L-BCAP29	ENST00000673757.1		c.1490-652T>C	intron	N/A	ENSP00000501026.1	A0A669KAY5

Frequencies

GnomAD3 genomes

AF:

0.752

AC:

114313

AN:

151986

Hom.:

43293

Cov.:

show subpopulations

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.:

AF XY:

0.752

AC XY:

55933

AN XY:

74340

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1461

2922

4384

5845

7306

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.9

(source)

DANN

Benign

0.44

PhyloP100

-0.62

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over