rs1689800

chr1-182199750-A-G

Variant summary

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

The ENST00000663078.1(LINC01344):n.269+4135T>C 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 0.337 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 ENST00000663078.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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=-0.95).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01344	ENST00000663078.1	n.269+4135T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.342

Alfa AF: 0.358 Hom.: 11903

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1689800; hg19: chr1-182168885;