20-6815572-C-T

Position:

• chr20-6815572-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 0.111 in 152,052 control chromosomes in the GnomAD database, including 1,246 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 0.11 (1246 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16807 AN: 151934 Hom.: 1243 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.111 AC: 16823 AN: 152052 Hom.: 1246 Cov.: 32 AF XY: 0.111 AC XY: 8223 AN XY: 74330

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.0880

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0818 Hom.: 861

Bravo AF: 0.116

Asia WGS AF: 0.138 AC: 478 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	0.43
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs996544; hg19: chr20-6796219;