rs858957

Variant names:

• chr2-176802611-A-T
• rs858957
• ENST00000428283.5:n.136+9461T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000428283.5(ENSG00000230552):​n.136+9461T>A variant causes a intron 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: ENSG00000230552 ENST00000428283.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.696
• Publications: 2 publications found

Genes affected

ENSG00000230552 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230552	ENST00000428283.5	n.136+9461T>A		intron_variant	Intron 2 of 5	1
ENSG00000230552	ENST00000451851.1	n.196+9461T>A		intron_variant	Intron 2 of 5	4
LINC01117	ENST00000652227.1	n.639+13248A>T		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.298 AC: 12308 AN: 41338

American (AMR) AF: 0.332 AC: 5050 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1651 AN: 3468

East Asian (EAS) AF: 0.0275 AC: 142 AN: 5168

South Asian (SAS) AF: 0.291 AC: 1398 AN: 4800

European-Finnish (FIN) AF: 0.363 AC: 3767 AN: 10380

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 32993 AN: 67818

Other (OTH) AF: 0.418 AC: 875 AN: 2094

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs858957; hg19: chr2-177667339;