rs858957

Positions:

• chr2-176802611-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428283.5(ENSG00000230552):​n.136+9461T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,486 control chromosomes in the GnomAD database, including 12,565 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 0.39 (12565 hom., cov: 29)
• Consequence: ENST00000428283.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696

Genes affected

(HGNC:):

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657778.1	n.167+9461T>A		intron_variant, non_coding_transcript_variant
LINC01117	ENST00000702503.1	n.657+13248A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58792 AN: 151368 Hom.: 12559 Cov.: 29

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.388 AC: 58833 AN: 151486 Hom.: 12565 Cov.: 29 AF XY: 0.378 AC XY: 27940 AN XY: 73986

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.418

Alfa AF: 0.423 Hom.: 1792

Bravo AF: 0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.12
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs858957; hg19: chr2-177667339;