rs4810796

Variant names:

• chr20-48459954-G-A
• rs4810796

Your query was ambiguous. Multiple possible variants found:

• chr20-48459954-G-A
• chr20-48459954-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 0.319 in 151,908 control chromosomes in the GnomAD database, including 8,172 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 0.32 (8172 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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: 0.319 AC: 48346 AN: 151790 Hom.: 8158 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.319 AC: 48389 AN: 151908 Hom.: 8172 Cov.: 32 AF XY: 0.328 AC XY: 24345 AN XY: 74236

African (AFR) AF: 0.274 AC: 11341 AN: 41386

American (AMR) AF: 0.463 AC: 7067 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.521 AC: 2678 AN: 5144

South Asian (SAS) AF: 0.361 AC: 1737 AN: 4814

European-Finnish (FIN) AF: 0.367 AC: 3863 AN: 10538

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19801 AN: 67976

Other (OTH) AF: 0.302 AC: 638 AN: 2110

Alfa AF: 0.301 Hom.: 18926

Bravo AF: 0.327

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.71
DANN	Benign	0.91
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4810796; hg19: chr20-47088200;