rs10177924

Variant names:

• chr2-156077041-A-G
• rs10177924
• ENST00000428651.2:n.160-52465T>C

Variant summary

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

The ENST00000428651.2(LINC01876):​n.160-52465T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,034 control chromosomes in the GnomAD database, including 6,088 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 0.28 (6088 hom., cov: 32)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-52465T>C		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.155-52434T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.160-52465T>C		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.153-52465T>C		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.269-52434T>C		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42398 AN: 151916 Hom.: 6092 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.279 AC: 42400 AN: 152034 Hom.: 6088 Cov.: 32 AF XY: 0.279 AC XY: 20700 AN XY: 74312

African (AFR) AF: 0.261 AC: 10800 AN: 41454

American (AMR) AF: 0.218 AC: 3326 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3470

East Asian (EAS) AF: 0.126 AC: 651 AN: 5164

South Asian (SAS) AF: 0.318 AC: 1535 AN: 4828

European-Finnish (FIN) AF: 0.333 AC: 3528 AN: 10584

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20552 AN: 67960

Other (OTH) AF: 0.271 AC: 572 AN: 2108

Alfa AF: 0.291 Hom.: 11653

Bravo AF: 0.267

Asia WGS AF: 0.257 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.77
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10177924; hg19: chr2-156933553;