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.

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.690+1671T>C	intron	N/A	NP_061332.2	E9PAJ1
DUS4L-BCAP29	NM_001371364.2		c.1489+1371T>C	intron	N/A	NP_001358293.1	A0A669KAY5
DUS4L-BCAP29	NM_001371365.2		c.1410+1671T>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.690+1671T>C	intron	N/A	ENSP00000005259.4	Q9UHQ4-1
DUS4L-BCAP29	ENST00000673665.1		c.1410+1671T>C	intron	N/A	ENSP00000501082.1	A0A669KB27
DUS4L-BCAP29	ENST00000673757.1		c.1489+1371T>C	intron	N/A	ENSP00000501026.1	A0A669KAY5

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over