rs812810

Variant names:

• chr2-7746748-C-T
• rs812810
• ENST00000811668.1:n.244-1940C>T

Variant summary

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

The ENST00000811668.1(LINC01871):​n.244-1940C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.902 in 152,186 control chromosomes in the GnomAD database, including 61,930 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 0.90 (61930 hom., cov: 31)
• Consequence: LINC01871 ENST00000811668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212
• Publications: 0 publications found

Genes affected

LINC01871 (HGNC:52690): (long intergenic non-protein coding RNA 1871)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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
LINC01871	ENST00000811668.1	n.244-1940C>T		intron_variant	Intron 2 of 2
LINC01871	ENST00000811669.1	n.240-1795C>T		intron_variant	Intron 2 of 2
LINC01871	ENST00000811670.1	n.52-1795C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137143 AN: 152068 Hom.: 61893 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.902 AC: 137231 AN: 152186 Hom.: 61930 Cov.: 31 AF XY: 0.901 AC XY: 67055 AN XY: 74408

African (AFR) AF: 0.866 AC: 35935 AN: 41494

American (AMR) AF: 0.909 AC: 13910 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3102 AN: 3470

East Asian (EAS) AF: 0.956 AC: 4940 AN: 5168

South Asian (SAS) AF: 0.894 AC: 4305 AN: 4816

European-Finnish (FIN) AF: 0.913 AC: 9663 AN: 10580

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62464 AN: 68030

Other (OTH) AF: 0.900 AC: 1904 AN: 2116

Alfa AF: 0.911 Hom.: 105287

Bravo AF: 0.900

Asia WGS AF: 0.911 AC: 3167 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	0.23
DANN	Benign	0.30
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs812810; hg19: chr2-7886879;