chr1-182290924-C-T

Position:

• chr1-182290924-C-T

Variant summary

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

The NR_104175.1(LINC01344):​n.410+22566G>A 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 0.292 in 152,054 control chromosomes in the GnomAD database, including 7,901 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 0.29 (7901 hom., cov: 32)
• Consequence: LINC01344 NR_104175.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01344	NR_104175.1	n.410+22566G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01344	ENST00000663078.1	n.48+19237G>A		intron_variant, non_coding_transcript_variant
LINC01344	ENST00000449842.2	n.410+22566G>A		intron_variant, non_coding_transcript_variant		3
LINC01344	ENST00000653755.1	n.90+2332G>A		intron_variant, non_coding_transcript_variant
LINC01344	ENST00000702781.1	n.378-12511G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44442 AN: 151936 Hom.: 7897 Cov.: 32

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.292 AC: 44452 AN: 152054 Hom.: 7901 Cov.: 32 AF XY: 0.291 AC XY: 21588 AN XY: 74298

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.328

Alfa AF: 0.355 Hom.: 5048

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.66
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10911048; hg19: chr1-182260059;