rs4813250

Variant names:

• chr20-16780960-G-T
• rs4813250

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 0.28 in 152,076 control chromosomes in the GnomAD database, including 6,682 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 0.28 (6682 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.349 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: 0.280 AC: 42608 AN: 151958 Hom.: 6679 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.280 AC: 42618 AN: 152076 Hom.: 6682 Cov.: 33 AF XY: 0.282 AC XY: 20928 AN XY: 74332

African (AFR) AF: 0.148 AC: 6153 AN: 41500

American (AMR) AF: 0.285 AC: 4351 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 887 AN: 3468

East Asian (EAS) AF: 0.128 AC: 661 AN: 5184

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4828

European-Finnish (FIN) AF: 0.419 AC: 4421 AN: 10554

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23956 AN: 67958

Other (OTH) AF: 0.271 AC: 572 AN: 2110

Alfa AF: 0.319 Hom.: 3030

Bravo AF: 0.265

Asia WGS AF: 0.198 AC: 689 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.59
DANN	Benign	0.63
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4813250; hg19: chr20-16761605;