rs4456770

Variant names:

• chr20-6671503-G-A
• rs4456770

Your query was ambiguous. Multiple possible variants found:

• chr20-6671503-G-A
• chr20-6671503-G-T

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 0.398 in 151,874 control chromosomes in the GnomAD database, including 13,104 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 0.40 (13104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.398 AC: 60350 AN: 151756 Hom.: 13101 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.398 AC: 60372 AN: 151874 Hom.: 13104 Cov.: 32 AF XY: 0.389 AC XY: 28833 AN XY: 74206

African (AFR) AF: 0.257 AC: 10648 AN: 41420

American (AMR) AF: 0.382 AC: 5828 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3472

East Asian (EAS) AF: 0.146 AC: 753 AN: 5150

South Asian (SAS) AF: 0.212 AC: 1021 AN: 4808

European-Finnish (FIN) AF: 0.461 AC: 4849 AN: 10518

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33913 AN: 67938

Other (OTH) AF: 0.391 AC: 825 AN: 2110

Alfa AF: 0.464 Hom.: 20997

Bravo AF: 0.390

Asia WGS AF: 0.216 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.34
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs4456770; hg19: chr20-6652150;