rs10911044

Positions:

• chr1-182286975-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104175.1(LINC01344):​n.410+26515A>G variant causes a intron, non coding transcript 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 NR_104175.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01344	NR_104175.1	n.410+26515A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01344	ENST00000663078.1	n.48+23186A>G		intron_variant, non_coding_transcript_variant
LINC01344	ENST00000449842.2	n.410+26515A>G		intron_variant, non_coding_transcript_variant		3
LINC01344	ENST00000653755.1	n.90+6281A>G		intron_variant, non_coding_transcript_variant
LINC01344	ENST00000702781.1	n.378-8562A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.326

Alfa AF: 0.384 Hom.: 14783

Bravo AF: 0.302

Asia WGS AF: 0.232 AC: 804 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	0.51
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911044; hg19: chr1-182256110;