rs10497171

Variant names:

• chr2-156114540-T-G
• rs10497171
• ENST00000428651.2:n.160-89964A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000428651.2(LINC01876):​n.160-89964A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,262 control chromosomes in the GnomAD database, including 91 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 0.031 (91 hom., cov: 32)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 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=-0.94).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0305 (4647/152262) while in subpopulation NFE AF = 0.047 (3195/68008). AF 95% confidence interval is 0.0456. There are 91 homozygotes in GnomAd4. There are 2132 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-89964A>C		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.155-89933A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.160-89964A>C		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.153-89964A>C		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.269-89933A>C		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4646 AN: 152144 Hom.: 91 Cov.: 32

Gnomad AFR AF: 0.00772

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.0102

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00933

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0305 AC: 4647 AN: 152262 Hom.: 91 Cov.: 32 AF XY: 0.0286 AC XY: 2132 AN XY: 74468

African (AFR) AF: 0.00770 AC: 320 AN: 41554

American (AMR) AF: 0.0424 AC: 649 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5182

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4818

European-Finnish (FIN) AF: 0.00933 AC: 99 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0470 AC: 3195 AN: 68008

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0408 Hom.: 30

Bravo AF: 0.0318

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.91
DANN	Benign	0.63
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10497171; hg19: chr2-156971052;