rs4953063

Variant names:

• chr2-44092594-G-A
• rs4953063

Your query was ambiguous. Multiple possible variants found:

• chr2-44092594-G-A
• chr2-44092594-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 0.492 in 151,892 control chromosomes in the GnomAD database, including 18,705 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 0.49 (18705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74696 AN: 151774 Hom.: 18687 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.492 AC: 74752 AN: 151892 Hom.: 18705 Cov.: 32 AF XY: 0.498 AC XY: 36937 AN XY: 74216

African (AFR) AF: 0.489 AC: 20246 AN: 41422

American (AMR) AF: 0.587 AC: 8968 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4043 AN: 5104

South Asian (SAS) AF: 0.482 AC: 2322 AN: 4822

European-Finnish (FIN) AF: 0.507 AC: 5340 AN: 10536

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30782 AN: 67960

Other (OTH) AF: 0.476 AC: 1004 AN: 2110

Alfa AF: 0.473 Hom.: 52697

Bravo AF: 0.503

Asia WGS AF: 0.568 AC: 1970 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.23
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs4953063; hg19: chr2-44319733;