rs4653637

Variant names:

• chr1-225436314-G-A
• rs4653637

Your query was ambiguous. Multiple possible variants found:

• chr1-225436314-G-A
• chr1-225436314-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.623 in 152,084 control chromosomes in the GnomAD database, including 29,805 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 0.62 (29805 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94662 AN: 151966 Hom.: 29803 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.623 AC: 94699 AN: 152084 Hom.: 29805 Cov.: 33 AF XY: 0.618 AC XY: 45922 AN XY: 74332

African (AFR) AF: 0.545 AC: 22582 AN: 41462

American (AMR) AF: 0.670 AC: 10251 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2535 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3653 AN: 5178

South Asian (SAS) AF: 0.425 AC: 2050 AN: 4820

European-Finnish (FIN) AF: 0.591 AC: 6245 AN: 10564

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45101 AN: 67988

Other (OTH) AF: 0.640 AC: 1350 AN: 2108

Alfa AF: 0.652 Hom.: 103866

Bravo AF: 0.633

Asia WGS AF: 0.553 AC: 1924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4653637; hg19: chr1-225624016;