rs10497176

Variant names:

• chr2-156066908-T-C
• rs10497176
• ENST00000428651.2:n.160-42332A>G

Variant summary

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

The ENST00000428651.2(LINC01876):​n.160-42332A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0624 in 152,198 control chromosomes in the GnomAD database, including 405 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 0.062 (405 hom., cov: 32)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 0 publications found

Genes affected

LINC01876 (HGNC:52695): (long intergenic non-protein coding RNA 1876)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-42332A>G		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.155-42301A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.160-42332A>G		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.153-42332A>G		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.269-42301A>G		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0624 AC: 9483 AN: 152080 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.0714

Gnomad EAS AF: 0.0385

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0425

Gnomad OTH AF: 0.0690

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

GnomAD4 genome AF: 0.0624 AC: 9501 AN: 152198 Hom.: 405 Cov.: 32 AF XY: 0.0613 AC XY: 4558 AN XY: 74406

African (AFR) AF: 0.113 AC: 4676 AN: 41538

American (AMR) AF: 0.0429 AC: 654 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0714 AC: 248 AN: 3472

East Asian (EAS) AF: 0.0386 AC: 200 AN: 5180

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4826

European-Finnish (FIN) AF: 0.0473 AC: 502 AN: 10602

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0425 AC: 2893 AN: 68006

Other (OTH) AF: 0.0682 AC: 144 AN: 2110

Alfa AF: 0.0501 Hom.: 32

Bravo AF: 0.0643

Asia WGS AF: 0.0360 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.069
DANN	Benign	0.64
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10497176; hg19: chr2-156923420;