Genetic Variant BCAP29:c.690+1671T>C (chr7-107615103-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.690+1671T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 407,354 control chromosomes in the GnomAD database, including 109,879 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 0.72 ( 39661 hom., cov: 32)

Exomes 𝑓: 0.74 ( 70218 hom. )

Consequence

BCAP29
NM_018844.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.150

Publications

7 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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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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAP29	NM_018844.4 link	c.690+1671T>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 link	c.690+1671T>C		intron_variant	Intron 7 of 7	1	NM_018844.4	ENSP00000005259.4
DUS4L-BCAP29	ENST00000673665.1 link	c.1410+1671T>C		intron_variant	Intron 12 of 12			ENSP00000501082.1

Frequencies

GnomAD3 genomes

AF:

0.722

AC:

109690

AN:

151990

Hom.:

39641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.744

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.679

Gnomad EAS

AF:

0.670

Gnomad SAS

AF:

0.844

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.727

GnomAD4 exome

AF:

0.738

AC:

188496

AN:

255246

Hom.:

70218

AF XY:

0.746

AC XY:

106892

AN XY:

143244

show subpopulations

African (AFR)

AF:

0.744

AC:

5278

AN:

7098

American (AMR)

AF:

0.729

AC:

15831

AN:

21720

Ashkenazi Jewish (ASJ)

AF:

0.662

AC:

5171

AN:

7816

East Asian (EAS)

AF:

0.677

AC:

5880

AN:

8690

South Asian (SAS)

AF:

0.835

AC:

43175

AN:

51688

European-Finnish (FIN)

AF:

0.727

AC:

7848

AN:

10794

Middle Eastern (MID)

AF:

0.760

AC:

1911

AN:

2516

European-Non Finnish (NFE)

AF:

0.713

AC:

94710

AN:

132926

Other (OTH)

AF:

0.724

AC:

8692

AN:

11998

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

2301

4603

6904

9206

11507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

584

1168

1752

2336

2920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.722

AC:

109756

AN:

152108

Hom.:

39661

Cov.:

AF XY:

0.723

AC XY:

53739

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.744

AC:

30857

AN:

41462

American (AMR)

AF:

0.716

AC:

10951

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.679

AC:

2357

AN:

3472

East Asian (EAS)

AF:

0.669

AC:

3462

AN:

5176

South Asian (SAS)

AF:

0.845

AC:

4074

AN:

4824

European-Finnish (FIN)

AF:

0.717

AC:

7586

AN:

10582

Middle Eastern (MID)

AF:

0.728

AC:

214

AN:

294

European-Non Finnish (NFE)

AF:

0.707

AC:

48093

AN:

67996

Other (OTH)

AF:

0.726

AC:

1531

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1585

3170

4756

6341

7926

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<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:

0.701

Hom.:

10513

Bravo

AF:

0.717

Asia WGS

AF:

0.743

AC:

2585

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

(source)

DANN

Benign

0.73

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over