rs4239771

Variant names:

• chr20-7279234-T-A
• rs4239771

Your query was ambiguous. Multiple possible variants found:

• chr20-7279234-T-A
• chr20-7279234-T-C
• chr20-7279234-T-G

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 151,844 control chromosomes in the GnomAD database, including 19,038 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 (19038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.602 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

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74672 AN: 151724 Hom.: 19002 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.492 AC: 74755 AN: 151844 Hom.: 19038 Cov.: 31 AF XY: 0.495 AC XY: 36706 AN XY: 74192

African (AFR) AF: 0.376 AC: 15588 AN: 41424

American (AMR) AF: 0.612 AC: 9336 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2194 AN: 5116

South Asian (SAS) AF: 0.524 AC: 2523 AN: 4816

European-Finnish (FIN) AF: 0.467 AC: 4914 AN: 10524

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36474 AN: 67922

Other (OTH) AF: 0.533 AC: 1126 AN: 2114

Alfa AF: 0.356 Hom.: 893

Bravo AF: 0.497

Asia WGS AF: 0.508 AC: 1760 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.76
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs4239771; hg19: chr20-7259881;