20-54174247-T-G

Variant names:

• chr20-54174247-T-G
• rs2762943

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.945 in 152,062 control chromosomes in the GnomAD database, including 67,963 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.94 (67963 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 20-54174247-T-G is Benign according to our data. Variant chr20-54174247-T-G is described in ClinVar as [Benign]. Clinvar id is 1238763.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 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: 0.945 AC: 143569 AN: 151946 Hom.: 67906 Cov.: 30

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.945 AC: 143685 AN: 152062 Hom.: 67963 Cov.: 30 AF XY: 0.945 AC XY: 70269 AN XY: 74336

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.959

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.914

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.938

Alfa AF: 0.931 Hom.: 17063

Bravo AF: 0.950

Asia WGS AF: 0.976 AC: 3395 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2762943; hg19: chr20-52790786;