rs4814966

Variant names:

• chr20-2094276-G-A
• rs4814966

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 0.802 in 152,152 control chromosomes in the GnomAD database, including 51,011 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 0.80 (51011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 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: 0.802 AC: 121967 AN: 152034 Hom.: 50979 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.802 AC: 122048 AN: 152152 Hom.: 51011 Cov.: 32 AF XY: 0.788 AC XY: 58636 AN XY: 74374

African (AFR) AF: 0.750 AC: 31108 AN: 41494

American (AMR) AF: 0.675 AC: 10318 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2928 AN: 3472

East Asian (EAS) AF: 0.149 AC: 767 AN: 5162

South Asian (SAS) AF: 0.575 AC: 2767 AN: 4810

European-Finnish (FIN) AF: 0.848 AC: 8983 AN: 10594

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62585 AN: 68020

Other (OTH) AF: 0.778 AC: 1642 AN: 2110

Alfa AF: 0.870 Hom.: 100009

Bravo AF: 0.784

Asia WGS AF: 0.360 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.23
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4814966; hg19: chr20-2074922;