chr20-54174247-T-G

Variant names:

• chr20-54174247-T-G
• rs2762943
• ENST00000655028.2:n.393-506T>G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000655028.2(ENSG00000286587):​n.393-506T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000286587 ENST00000655028.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.08
• Publications: 16 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655028.2. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000286587	ENST00000655028.2		n.393-506T>G		intron	N/A
	ENSG00000286587	ENST00000792273.1		n.288+5676T>G		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.279-4145T>G		intron	N/A

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

African (AFR) AF: 0.986 AC: 40937 AN: 41520

American (AMR) AF: 0.953 AC: 14587 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3330 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5102 AN: 5106

South Asian (SAS) AF: 0.931 AC: 4487 AN: 4818

European-Finnish (FIN) AF: 0.914 AC: 9695 AN: 10608

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62481 AN: 67918

Other (OTH) AF: 0.938 AC: 1977 AN: 2108

Alfa AF: 0.936 Hom.: 28185

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.36
PhyloP100		1.1
PromoterAI		-0.26	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2762943; hg19: chr20-52790786;