1-182112825-C-T

Variant names:

• chr1-182112825-C-T
• rs10911021
• ENST00000663078.1:n.409-12122G>A

Variant summary

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

The ENST00000663078.1(LINC01344):​n.409-12122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,920 control chromosomes in the GnomAD database, including 9,941 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 0.35 (9941 hom., cov: 31)
• Consequence: LINC01344 ENST00000663078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 50 publications found

Genes affected

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

ENSG00000225982 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371642	XR_922341.3	n.141-2426C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01344	ENST00000663078.1	n.409-12122G>A		intron_variant	Intron 3 of 4
LINC01344	ENST00000756661.1	n.321-12122G>A		intron_variant	Intron 3 of 4
ENSG00000225982	ENST00000756806.1	n.194-2426C>T		intron_variant	Intron 1 of 2
ENSG00000225982	ENST00000756807.1	n.284-2426C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53661 AN: 151802 Hom.: 9898 Cov.: 31

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.354 AC: 53769 AN: 151920 Hom.: 9941 Cov.: 31 AF XY: 0.351 AC XY: 26030 AN XY: 74252

African (AFR) AF: 0.481 AC: 19911 AN: 41396

American (AMR) AF: 0.318 AC: 4858 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5164

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4822

European-Finnish (FIN) AF: 0.310 AC: 3268 AN: 10552

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20955 AN: 67930

Other (OTH) AF: 0.322 AC: 678 AN: 2104

Alfa AF: 0.319 Hom.: 35314

Bravo AF: 0.357

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10911021; hg19: chr1-182081960;