ENST00000420760.2:n.377-27419G>A

Variant names:

• chr1-182231524-C-T
• rs10494545
• ENST00000420760.2:n.377-27419G>A

Variant summary

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

The ENST00000420760.2(LINC01344):​n.377-27419G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,010 control chromosomes in the GnomAD database, including 3,891 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 0.21 (3891 hom., cov: 31)
• Consequence: LINC01344 ENST00000420760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01344	NR_104175.1	n.411-27419G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01344	ENST00000420760.2	n.377-27419G>A		intron_variant	Intron 2 of 3	3
LINC01344	ENST00000449842.2	n.411-27419G>A		intron_variant	Intron 2 of 4	3
LINC01344	ENST00000608183.1	n.118+11600G>A		intron_variant	Intron 2 of 16	2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32261 AN: 151892 Hom.: 3891 Cov.: 31

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.212 AC: 32258 AN: 152010 Hom.: 3891 Cov.: 31 AF XY: 0.214 AC XY: 15900 AN XY: 74304

African (AFR) AF: 0.0850 AC: 3525 AN: 41482

American (AMR) AF: 0.266 AC: 4058 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 890 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1981 AN: 5152

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4816

European-Finnish (FIN) AF: 0.211 AC: 2222 AN: 10548

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17624 AN: 67974

Other (OTH) AF: 0.235 AC: 496 AN: 2108

Alfa AF: 0.244 Hom.: 20408

Bravo AF: 0.209

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10494545; hg19: chr1-182200659;