chr20-641181-T-C

Variant names:

• chr20-641181-T-C
• rs6076864

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 0.152 in 152,208 control chromosomes in the GnomAD database, including 1,923 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 0.15 (1923 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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: 0.152 AC: 23126 AN: 152090 Hom.: 1924 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0769

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.152 AC: 23132 AN: 152208 Hom.: 1923 Cov.: 31 AF XY: 0.149 AC XY: 11112 AN XY: 74414

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0776

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.148

Alfa AF: 0.173 Hom.: 2935

Bravo AF: 0.146

Asia WGS AF: 0.0400 AC: 139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6076864; hg19: chr20-621825;