dbSNP rs11063455: ENSG00000256654:n.573-7710G>A (chr12-5002440-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000638821.1(ENSG00000256654):n.573-7710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,204 control chromosomes in the GnomAD database, including 2,048 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 0.16 ( 2048 hom., cov: 32)

Consequence

ENSG00000256654
ENST00000638821.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.18

Publications

4 publications found

Variant links:

Genes affected

ENSG00000256654 (HGNC:):

ENSG00000256654 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=-1.03).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000256654	ENST00000638821.1 link	n.573-7710G>A	intron_variant	Intron 1 of 1	5
ENSG00000256654	ENST00000639005.1 link	n.685-19248G>A	intron_variant	Intron 2 of 5	5
ENSG00000256654	ENST00000640862.1 link	n.704-20051G>A	intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.160

AC:

24391

AN:

152084

Hom.:

2038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.125

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.181

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.168

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.161

AC:

24430

AN:

152204

Hom.:

2048

Cov.:

AF XY:

0.158

AC XY:

11742

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.126

AC:

5221

AN:

41534

American (AMR)

AF:

0.125

AC:

1908

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

680

AN:

3472

East Asian (EAS)

AF:

0.139

AC:

720

AN:

5182

South Asian (SAS)

AF:

0.110

AC:

530

AN:

4820

European-Finnish (FIN)

AF:

0.181

AC:

1918

AN:

10588

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12948

AN:

68006

Other (OTH)

AF:

0.173

AC:

366

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1059

2118

3178

4237

5296

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.180

Hom.:

6786

Bravo

AF:

0.156

Asia WGS

AF:

0.123

AC:

427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.014

(source)

DANN

Benign

0.59

PhyloP100

-5.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over