chr20-46310212-T-C

Position:

• chr20-46310212-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 0.741 in 152,212 control chromosomes in the GnomAD database, including 41,855 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 0.74 (41855 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 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: 0.741 AC: 112660 AN: 152094 Hom.: 41824 Cov.: 34

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.741 AC: 112743 AN: 152212 Hom.: 41855 Cov.: 34 AF XY: 0.740 AC XY: 55090 AN XY: 74428

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.640

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.775

Alfa AF: 0.744 Hom.: 83672

Bravo AF: 0.744

Asia WGS AF: 0.691 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6032769; hg19: chr20-44938851;