10-2315508-G-A

Variant names:

• chr10-2315508-G-A
• rs12412942
• ENST00000721486.1:n.285+79G>A

Variant summary

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

The ENST00000721486.1(ENSG00000294151):​n.285+79G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,184 control chromosomes in the GnomAD database, including 21,308 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 0.52 (21308 hom., cov: 34)
• Consequence: ENSG00000294151 ENST00000721486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 8 publications found

Genes affected

ENSG00000294151 (HGNC:):

LINC00701 (HGNC:44674): (long intergenic non-protein coding RNA 701)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 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
ENSG00000294151	ENST00000721486.1	n.285+79G>A		intron_variant	Intron 1 of 4
LINC00701	ENST00000721390.1	n.-154C>T		upstream_gene_variant
LINC00701	ENST00000721391.1	n.-223C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79236 AN: 152066 Hom.: 21311 Cov.: 34

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.521 AC: 79251 AN: 152184 Hom.: 21308 Cov.: 34 AF XY: 0.526 AC XY: 39101 AN XY: 74402

African (AFR) AF: 0.384 AC: 15934 AN: 41520

American (AMR) AF: 0.496 AC: 7587 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1698 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2744 AN: 5162

South Asian (SAS) AF: 0.572 AC: 2760 AN: 4824

European-Finnish (FIN) AF: 0.659 AC: 6989 AN: 10604

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39704 AN: 67998

Other (OTH) AF: 0.526 AC: 1109 AN: 2110

Alfa AF: 0.560 Hom.: 100554

Bravo AF: 0.503

Asia WGS AF: 0.523 AC: 1821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.42
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12412942; hg19: chr10-2357702;