20-54174247-T-G

Position:

• chr20-54174247-T-G

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: intergenic_region
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.08

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.54174247T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

- -

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;