rs1203952

Variant names:

• chr20-22633494-G-A
• rs1203952

Your query was ambiguous. Multiple possible variants found:

• chr20-22633494-G-A
• chr20-22633494-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.699 in 152,128 control chromosomes in the GnomAD database, including 38,671 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 0.70 (38671 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 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: 0.699 AC: 106317 AN: 152010 Hom.: 38666 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.699 AC: 106353 AN: 152128 Hom.: 38671 Cov.: 33 AF XY: 0.705 AC XY: 52419 AN XY: 74382

African (AFR) AF: 0.484 AC: 20059 AN: 41442

American (AMR) AF: 0.756 AC: 11562 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2557 AN: 3472

East Asian (EAS) AF: 0.771 AC: 3985 AN: 5166

South Asian (SAS) AF: 0.850 AC: 4098 AN: 4822

European-Finnish (FIN) AF: 0.812 AC: 8601 AN: 10598

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53084 AN: 68014

Other (OTH) AF: 0.697 AC: 1471 AN: 2110

Alfa AF: 0.747 Hom.: 44853

Bravo AF: 0.683

Asia WGS AF: 0.756 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.79
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1203952; hg19: chr20-22614132;