rs2809811

Variant names:

• chr1-100567394-G-A
• rs2809811
• ENST00000773974.1:n.165-8101C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-100567394-G-A
• chr1-100567394-G-T

Variant summary

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

The ENST00000773974.1(LINC01349):​n.165-8101C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,208 control chromosomes in the GnomAD database, including 64,152 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 0.91 (64152 hom., cov: 32)
• Consequence: LINC01349 ENST00000773974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899
• Publications: 1 publications found

Genes affected

LINC01349 (HGNC:50568): (long intergenic non-protein coding RNA 1349)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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
LINC01349	ENST00000773974.1	n.165-8101C>T		intron_variant	Intron 3 of 3
LINC01349	ENST00000773975.1	n.125-8101C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138003 AN: 152090 Hom.: 64124 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.927

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

GnomAD4 genome AF: 0.907 AC: 138079 AN: 152208 Hom.: 64152 Cov.: 32 AF XY: 0.910 AC XY: 67730 AN XY: 74434

African (AFR) AF: 0.680 AC: 28206 AN: 41468

American (AMR) AF: 0.961 AC: 14685 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 3470 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5192 AN: 5192

South Asian (SAS) AF: 0.999 AC: 4827 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10614 AN: 10616

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67929 AN: 68028

Other (OTH) AF: 0.928 AC: 1959 AN: 2112

Alfa AF: 0.969 Hom.: 106680

Bravo AF: 0.894

Asia WGS AF: 0.977 AC: 3382 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.19
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs2809811; hg19: chr1-101032950;