20-6934267-T-C

Position:

• chr20-6934267-T-C

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 0.792 in 152,124 control chromosomes in the GnomAD database, including 48,327 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 (48327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 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: 0.792 AC: 120352 AN: 152006 Hom.: 48299 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.792 AC: 120435 AN: 152124 Hom.: 48327 Cov.: 33 AF XY: 0.791 AC XY: 58816 AN XY: 74386

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.788

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.780

Alfa AF: 0.813 Hom.: 6454

Bravo AF: 0.786

Asia WGS AF: 0.635 AC: 2194 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs717087; hg19: chr20-6914914;