rs10911044

Variant names:

• chr1-182286975-T-C
• rs10911044
• ENST00000420760.2:n.376+26515A>G

Variant summary

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

The ENST00000420760.2(LINC01344):​n.376+26515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,994 control chromosomes in the GnomAD database, including 8,359 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 0.31 (8359 hom., cov: 31)
• Consequence: LINC01344 ENST00000420760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 3 publications found

Genes affected

LINC01344 (HGNC:50554): (long intergenic non-protein coding RNA 1344)

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 (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420760.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01344	NR_104175.1		n.410+26515A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01344	ENST00000420760.2	TSL:3	n.376+26515A>G		intron	N/A
	LINC01344	ENST00000449842.2	TSL:3	n.410+26515A>G		intron	N/A
	LINC01344	ENST00000653755.1		n.90+6281A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46593 AN: 151878 Hom.: 8356 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.307 AC: 46606 AN: 151994 Hom.: 8359 Cov.: 31 AF XY: 0.305 AC XY: 22657 AN XY: 74284

African (AFR) AF: 0.115 AC: 4792 AN: 41500

American (AMR) AF: 0.338 AC: 5152 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5154

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4816

European-Finnish (FIN) AF: 0.371 AC: 3918 AN: 10560

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27607 AN: 67922

Other (OTH) AF: 0.326 AC: 687 AN: 2108

Alfa AF: 0.374 Hom.: 19643

Bravo AF: 0.302

Asia WGS AF: 0.232 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.51
DANN	Benign	0.49
PhyloP100		-2.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10911044;

hg19: chr1-182256110;