dbSNP rs7578654: ENSG00000282890:n.493-125168A>C (chr2-49283034-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000634588.1(ENSG00000282890):n.493-125168A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 494,086 control chromosomes in the GnomAD database, including 45,741 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 0.45 ( 15268 hom., cov: 33)

Exomes 𝑓: 0.42 ( 30473 hom. )

Consequence

ENSG00000282890
ENST00000634588.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.394

Variant links:

Genes affected

ENSG00000282890 (HGNC:58158):

ENSG00000282890 links:

ENSG00000282998 (HGNC:):

ENSG00000282998 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282890	ENST00000634588.1 link	n.493-125168A>C		intron_variant	Intron 2 of 4	5
ENSG00000282998	ENST00000635306.1 link	n.407+48840T>G		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

67935

AN:

151536

Hom.:

15245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.440

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.437

GnomAD3 exomes

AF:

0.419

AC:

91900

AN:

219402

Hom.:

19609

AF XY:

0.419

AC XY:

50990

AN XY:

121820

show subpopulations

Gnomad AFR exome

AF:

0.481

Gnomad AMR exome

AF:

0.381

Gnomad ASJ exome

AF:

0.396

Gnomad EAS exome

AF:

0.376

Gnomad SAS exome

AF:

0.404

Gnomad FIN exome

AF:

0.424

Gnomad NFE exome

AF:

0.437

Gnomad OTH exome

AF:

0.401

GnomAD4 exome

AF:

0.417

AC:

142816

AN:

342432

Hom.:

30473

Cov.:

AF XY:

0.417

AC XY:

82541

AN XY:

197834

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.378

Gnomad4 ASJ exome

AF:

0.393

Gnomad4 EAS exome

AF:

0.369

Gnomad4 SAS exome

AF:

0.403

Gnomad4 FIN exome

AF:

0.421

Gnomad4 NFE exome

AF:

0.432

Gnomad4 OTH exome

AF:

0.412

GnomAD4 genome

AF:

0.448

AC:

68010

AN:

151654

Hom.:

15268

Cov.:

AF XY:

0.447

AC XY:

33095

AN XY:

74102

show subpopulations

Gnomad4 AFR

AF:

0.488

Gnomad4 AMR

AF:

0.390

Gnomad4 ASJ

AF:

0.407

Gnomad4 EAS

AF:

0.391

Gnomad4 SAS

AF:

0.425

Gnomad4 FIN

AF:

0.440

Gnomad4 NFE

AF:

0.448

Gnomad4 OTH

AF:

0.436

Alfa

AF:

0.438

Hom.:

31182

Bravo

AF:

0.446

Asia WGS

AF:

0.424

AC:

1475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

9.3

DANN

Benign

0.69

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over