dbSNP rs4808075: ENSG00000269307:n.*400+2573T>C (chr19-17279482-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 ENST00000596542.1(ENSG00000269307):n.*400+2573T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 161,458 control chromosomes in the GnomAD database, including 5,383 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 0.25 ( 5089 hom., cov: 31)

Exomes 𝑓: 0.22 ( 294 hom. )

Consequence

ENSG00000269307
ENST00000596542.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

19 publications found

Variant links:

Genes affected

ENSG00000269307 (HGNC:):

ENSG00000269307 links:

USHBP1 (HGNC:24058): (USH1 protein network component harmonin binding protein 1) Enables PDZ domain binding activity. [provided by Alliance of Genome Resources, Apr 2022]

USHBP1 links:

BABAM1 (HGNC:25008): (BRISC and BRCA1 A complex member 1) Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; positive regulation of DNA repair; and protein K63-linked deubiquitination. Located in cytosol and nuclear body. Part of BRCA1-A complex and BRISC complex. [provided by Alliance of Genome Resources, Apr 2022]

BABAM1 links:

Genome browser will be placed here

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000596542.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BABAM1	NM_014173.4	MANE Select	c.*434T>C	downstream_gene	N/A	NP_054892.2	Q9NWV8-1
BABAM1	NM_001033549.3		c.*434T>C	downstream_gene	N/A	NP_001028721.1	Q9NWV8-1
BABAM1	NM_001288756.2		c.*434T>C	downstream_gene	N/A	NP_001275685.1	Q9NWV8-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENSG00000269307	ENST00000596542.1	TSL:2	n.*400+2573T>C	intron	N/A	ENSP00000469159.2	M0QXG9
USHBP1	ENST00000598309.1	TSL:4	c.-201+3054A>G	intron	N/A	ENSP00000471680.1	M0R172
BABAM1	ENST00000594247.5	TSL:5	n.*499-1754T>C	intron	N/A	ENSP00000469527.1	M0QXG9

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37960

AN:

151880

Hom.:

5086

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.206

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.295

Gnomad OTH

AF:

0.250

GnomAD4 exome

AF:

0.219

AC:

2073

AN:

9460

Hom.:

294

AF XY:

0.220

AC XY:

1058

AN XY:

4808

show subpopulations

African (AFR)

AF:

0.223

AC:

AN:

310

American (AMR)

AF:

0.112

AC:

AN:

438

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

101

AN:

352

East Asian (EAS)

AF:

0.00202

AC:

AN:

496

South Asian (SAS)

AF:

0.130

AC:

AN:

554

European-Finnish (FIN)

AF:

0.290

AC:

109

AN:

376

Middle Eastern (MID)

AF:

0.111

AC:

AN:

European-Non Finnish (NFE)

AF:

0.246

AC:

1549

AN:

6298

Other (OTH)

AF:

0.198

AC:

119

AN:

600

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

166

249

332

415

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.250

AC:

37968

AN:

151998

Hom.:

5089

Cov.:

AF XY:

0.245

AC XY:

18208

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.228

AC:

9450

AN:

41426

American (AMR)

AF:

0.178

AC:

2717

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

955

AN:

3470

East Asian (EAS)

AF:

0.00309

AC:

AN:

5182

South Asian (SAS)

AF:

0.138

AC:

665

AN:

4816

European-Finnish (FIN)

AF:

0.315

AC:

3326

AN:

10566

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.295

AC:

20076

AN:

67972

Other (OTH)

AF:

0.249

AC:

525

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1415

2830

4244

5659

7074

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.202

Hom.:

791

Bravo

AF:

0.238

Asia WGS

AF:

0.0830

AC:

291

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.80

(source)

DANN

Benign

0.62

PhyloP100

-1.5

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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