20-50496472-T-C

Position:

• chr20-50496472-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 0.844 in 145,766 control chromosomes in the GnomAD database, including 51,538 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 0.84 (51538 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.873 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: 0.844 AC: 122966 AN: 145682 Hom.: 51512 Cov.: 24

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.844 AC: 123031 AN: 145766 Hom.: 51538 Cov.: 24 AF XY: 0.845 AC XY: 60036 AN XY: 71026

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.892

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.842

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.842

Alfa AF: 0.771 Hom.: 1460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4811078; hg19: chr20-49113009;