rs585017

Positions:

• chr2-20446871-G-A
• chr2-20446871-G-C
• chr2-20446871-G-T

Variant summary

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

The ENST00000702995.1(ENSG00000290108):​n.23C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 151,996 control chromosomes in the GnomAD database, including 44,520 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.76 (44520 hom., cov: 33)
• Consequence: ENSG00000290108 ENST00000702995.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.202

Genes affected

ENSG00000290108 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BP6: Variant 2-20446871-G-A is Benign according to our data. Variant chr2-20446871-G-A is described in ClinVar as [Benign]. Clinvar id is 1271789.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20446871G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290108	ENST00000702995.1	n.23C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116005 AN: 151878 Hom.: 44463 Cov.: 33

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.764 AC: 116123 AN: 151996 Hom.: 44520 Cov.: 33 AF XY: 0.769 AC XY: 57126 AN XY: 74288

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.812

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.766

Alfa AF: 0.651 Hom.: 1809

Bravo AF: 0.770

Asia WGS AF: 0.860 AC: 2988 AN: 3476

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

May 14, 2021

This variant is associated with the following publications: (PMID: 16642435) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.2
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs585017; hg19: chr2-20646632;