20-43665973-T-C

Variant names:

• chr20-43665973-T-C
• rs619289

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 0.783 in 151,516 control chromosomes in the GnomAD database, including 46,885 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 0.78 (46885 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 28 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 = 0.833 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: 0.783 AC: 118535 AN: 151398 Hom.: 46863 Cov.: 27

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.783 AC: 118601 AN: 151516 Hom.: 46885 Cov.: 27 AF XY: 0.785 AC XY: 58096 AN XY: 73962

African (AFR) AF: 0.671 AC: 27663 AN: 41236

American (AMR) AF: 0.766 AC: 11637 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2729 AN: 3472

East Asian (EAS) AF: 0.799 AC: 4106 AN: 5138

South Asian (SAS) AF: 0.813 AC: 3904 AN: 4802

European-Finnish (FIN) AF: 0.858 AC: 8972 AN: 10454

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 56964 AN: 67922

Other (OTH) AF: 0.771 AC: 1621 AN: 2102

Alfa AF: 0.811 Hom.: 147159

Bravo AF: 0.768

Asia WGS AF: 0.776 AC: 2699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.60
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs619289; hg19: chr20-42294613;