20-240377-T-G

Variant names:

• chr20-240377-T-G
• rs10485819

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 0.175 in 151,658 control chromosomes in the GnomAD database, including 2,714 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 0.18 (2714 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26554 AN: 151544 Hom.: 2713 Cov.: 30

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0805

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.175 AC: 26559 AN: 151658 Hom.: 2714 Cov.: 30 AF XY: 0.175 AC XY: 12971 AN XY: 74112

African (AFR) AF: 0.288 AC: 11903 AN: 41282

American (AMR) AF: 0.137 AC: 2091 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0805 AC: 279 AN: 3466

East Asian (EAS) AF: 0.191 AC: 986 AN: 5160

South Asian (SAS) AF: 0.201 AC: 964 AN: 4792

European-Finnish (FIN) AF: 0.153 AC: 1598 AN: 10468

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8329 AN: 67958

Other (OTH) AF: 0.143 AC: 302 AN: 2108

Alfa AF: 0.121 Hom.: 747

Bravo AF: 0.177

Asia WGS AF: 0.205 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.86
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs10485819; hg19: chr20-221018;