rs4816025

Variant names:

• chr20-7869391-G-A
• rs4816025

Your query was ambiguous. Multiple possible variants found:

• chr20-7869391-G-A
• chr20-7869391-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 0.538 in 152,104 control chromosomes in the GnomAD database, including 25,909 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 0.54 (25909 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 2 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 = 0.714 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: 0.539 AC: 81872 AN: 151984 Hom.: 25913 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.538 AC: 81879 AN: 152104 Hom.: 25909 Cov.: 33 AF XY: 0.538 AC XY: 40010 AN XY: 74362

African (AFR) AF: 0.214 AC: 8888 AN: 41500

American (AMR) AF: 0.556 AC: 8488 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2258 AN: 3472

East Asian (EAS) AF: 0.256 AC: 1323 AN: 5160

South Asian (SAS) AF: 0.459 AC: 2216 AN: 4826

European-Finnish (FIN) AF: 0.740 AC: 7830 AN: 10586

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48871 AN: 67978

Other (OTH) AF: 0.552 AC: 1167 AN: 2114

Alfa AF: 0.592 Hom.: 4769

Bravo AF: 0.509

Asia WGS AF: 0.331 AC: 1152 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4816025; hg19: chr20-7850038;