20-46006406-G-T

Variant names:

• chr20-46006406-G-T
• rs8113877

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 0.542 in 151,962 control chromosomes in the GnomAD database, including 23,352 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 0.54 (23352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 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: 0.542 AC: 82345 AN: 151844 Hom.: 23347 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.0347

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.542 AC: 82372 AN: 151962 Hom.: 23352 Cov.: 32 AF XY: 0.532 AC XY: 39489 AN XY: 74282

African (AFR) AF: 0.538 AC: 22263 AN: 41412

American (AMR) AF: 0.537 AC: 8203 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1964 AN: 3472

East Asian (EAS) AF: 0.0344 AC: 178 AN: 5176

South Asian (SAS) AF: 0.404 AC: 1949 AN: 4822

European-Finnish (FIN) AF: 0.499 AC: 5260 AN: 10534

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40617 AN: 67944

Other (OTH) AF: 0.552 AC: 1165 AN: 2112

Alfa AF: 0.463 Hom.: 1743

Bravo AF: 0.540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.47
DANN	Benign	0.18
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs8113877; hg19: chr20-44635045;