rs6100223

chr20-58797137-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.825 in 152,164 control chromosomes in the GnomAD database, including 52,409 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 0.83 (52409 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125492 AN: 152046 Hom.: 52356 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.825 AC: 125603 AN: 152164 Hom.: 52409 Cov.: 31 AF XY: 0.823 AC XY: 61253 AN XY: 74382

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.779

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.801

Alfa AF: 0.804 Hom.: 7815

Bravo AF: 0.829

Asia WGS AF: 0.808 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.2
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6100223; hg19: chr20-57372192; COSMIC: COSV60105493;