ENST00000420760.2:n.376+22566G>A

Variant names:

• chr1-182290924-C-T
• rs10911048
• ENST00000420760.2:n.376+22566G>A

Variant summary

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

The ENST00000420760.2(LINC01344):​n.376+22566G>A variant causes a intron 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 ENST00000420760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 1 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=-0.87).
• 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 rank	MANE	Protein	UniProt
LINC01344	NR_104175.1	n.410+22566G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01344	ENST00000420760.2	n.376+22566G>A		intron_variant	Intron 2 of 3	3
LINC01344	ENST00000449842.2	n.410+22566G>A		intron_variant	Intron 2 of 4	3
LINC01344	ENST00000653755.1	n.90+2332G>A		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.0861 AC: 3573 AN: 41506

American (AMR) AF: 0.350 AC: 5350 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1399 AN: 5174

South Asian (SAS) AF: 0.271 AC: 1302 AN: 4812

European-Finnish (FIN) AF: 0.347 AC: 3659 AN: 10544

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26737 AN: 67956

Other (OTH) AF: 0.328 AC: 694 AN: 2114

Alfa AF: 0.358 Hom.: 5613

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10911048; hg19: chr1-182260059;