rs10495717

Variant names:

• chr2-21702195-T-C
• rs10495717
• ENST00000435237.1:n.194-97162T>C

Variant summary

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

The ENST00000435237.1(ENSG00000231204):​n.194-97162T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,644 control chromosomes in the GnomAD database, including 5,881 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 0.20 (5881 hom., cov: 31)
• Consequence: ENSG00000231204 ENST00000435237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 3 publications found

Genes affected

ENSG00000231204 (HGNC:):

LINC01822 (HGNC:52627): (long intergenic non-protein coding RNA 1822)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01822	NR_038837.1	n.236+7954A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231204	ENST00000435237.1	n.194-97162T>C		intron_variant	Intron 3 of 5	3
LINC01822	ENST00000435682.2	n.321+7954A>G		intron_variant	Intron 2 of 2	2
LINC01822	ENST00000663972.1	n.214+7954A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30986 AN: 151526 Hom.: 5856 Cov.: 31

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0514

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.205 AC: 31053 AN: 151644 Hom.: 5881 Cov.: 31 AF XY: 0.198 AC XY: 14675 AN XY: 74132

African (AFR) AF: 0.505 AC: 20860 AN: 41322

American (AMR) AF: 0.149 AC: 2268 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3466

East Asian (EAS) AF: 0.0509 AC: 261 AN: 5124

South Asian (SAS) AF: 0.0448 AC: 216 AN: 4818

European-Finnish (FIN) AF: 0.0425 AC: 451 AN: 10618

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0904 AC: 6126 AN: 67796

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.113 Hom.: 1015

Bravo AF: 0.228

Asia WGS AF: 0.0870 AC: 302 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.51
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10495717; hg19: chr2-21925067;