dbSNP rs1420023: ENSG00000256658:n.283+46G>T (chr12-12723177-C-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000726600.1(ENSG00000256658):n.283+46G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00618 in 151,834 control chromosomes in the GnomAD database, including 8 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 0.0062 ( 8 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

ENSG00000256658
ENST00000726600.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.45

Publications

17 publications found

Variant links:

Genes affected

ENSG00000256658 (HGNC:):

ENSG00000256658 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BS2

High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369663	XR_931366.4 link	n.1901+46G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256658	ENST00000726600.1 link	n.283+46G>T		intron_variant	Intron 2 of 2
ENSG00000256658	ENST00000542291.1 link	n.*120G>T		downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00618

AC:

937

AN:

151722

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00604

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.000574

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00803

Gnomad OTH

AF:

0.00673

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

GnomAD4 genome

AF:

0.00618

AC:

939

AN:

151834

Hom.:

Cov.:

AF XY:

0.00609

AC XY:

452

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.00145

AC:

AN:

41386

American (AMR)

AF:

0.00604

AC:

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.0418

AC:

145

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5178

South Asian (SAS)

AF:

0.0147

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.000574

AC:

AN:

10446

Middle Eastern (MID)

AF:

0.0137

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00803

AC:

546

AN:

67982

Other (OTH)

AF:

0.00667

AC:

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

137

182

228

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome 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

Alfa

AF:

0.000716

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

0.0090

(source)

DANN

Benign

0.76

PhyloP100

-3.4

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