1-182199750-A-G

Variant names:

• chr1-182199750-A-G
• rs1689800
• ENST00000420760.2:n.597+4135T>C

Variant summary

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

The ENST00000420760.2(LINC01344):​n.597+4135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,888 control chromosomes in the GnomAD database, including 8,687 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 0.34 (8687 hom., cov: 32)
• Consequence: LINC01344 ENST00000420760.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 75 publications found

Genes affected

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

ENSG00000289573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01344	ENST00000420760.2	n.597+4135T>C		intron_variant	Intron 3 of 3	3
LINC01344	ENST00000449842.2	n.631+4135T>C		intron_variant	Intron 3 of 4	3
LINC01344	ENST00000608183.1	n.576+4135T>C		intron_variant	Intron 5 of 16	2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51191 AN: 151770 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.337 AC: 51235 AN: 151888 Hom.: 8687 Cov.: 32 AF XY: 0.333 AC XY: 24697 AN XY: 74188

African (AFR) AF: 0.319 AC: 13217 AN: 41376

American (AMR) AF: 0.357 AC: 5443 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1384 AN: 5156

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4814

European-Finnish (FIN) AF: 0.255 AC: 2694 AN: 10564

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24768 AN: 67934

Other (OTH) AF: 0.342 AC: 723 AN: 2114

Alfa AF: 0.352 Hom.: 29771

Bravo AF: 0.344

Asia WGS AF: 0.248 AC: 865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.25
DANN	Benign	0.74
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1689800; hg19: chr1-182168885;