20-50496472-T-C

Variant names:

• chr20-50496472-T-C
• rs4811078

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.871 AC: 33827 AN: 38850

American (AMR) AF: 0.886 AC: 13130 AN: 14818

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3045 AN: 3412

East Asian (EAS) AF: 0.613 AC: 2985 AN: 4870

South Asian (SAS) AF: 0.842 AC: 3892 AN: 4622

European-Finnish (FIN) AF: 0.853 AC: 8222 AN: 9644

Middle Eastern (MID) AF: 0.870 AC: 247 AN: 284

European-Non Finnish (NFE) AF: 0.832 AC: 55215 AN: 66342

Other (OTH) AF: 0.842 AC: 1705 AN: 2024

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
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4811078; hg19: chr20-49113009;