20-38345681-C-T

Variant names:

• chr20-38345681-C-T
• rs2232571

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 0.793 in 152,030 control chromosomes in the GnomAD database, including 48,016 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 0.79 (48016 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.841 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: 0.793 AC: 120449 AN: 151912 Hom.: 48003 Cov.: 30

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.793 AC: 120503 AN: 152030 Hom.: 48016 Cov.: 30 AF XY: 0.792 AC XY: 58856 AN XY: 74322

African (AFR) AF: 0.721 AC: 29852 AN: 41426

American (AMR) AF: 0.854 AC: 13033 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2823 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3648 AN: 5176

South Asian (SAS) AF: 0.699 AC: 3359 AN: 4804

European-Finnish (FIN) AF: 0.850 AC: 8996 AN: 10586

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55977 AN: 67986

Other (OTH) AF: 0.815 AC: 1717 AN: 2108

Alfa AF: 0.818 Hom.: 77397

Bravo AF: 0.792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs2232571; hg19: chr20-36974084;