rs2795421

Positions:

• chr1-232747389-C-T

Variant summary

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

The ENST00000659372.1(LINC01744):​n.224+3687G>A 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 0.865 in 152,212 control chromosomes in the GnomAD database, including 57,607 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 0.86 (57607 hom., cov: 33)
• Consequence: LINC01744 ENST00000659372.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

Genes affected

LINC01744 (HGNC:52532): (long intergenic non-protein coding RNA 1744)

LOC107983960 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983960	XR_949277.1	n.265-2587C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01744	ENST00000659372.1	n.224+3687G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131555 AN: 152094 Hom.: 57574 Cov.: 33

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.865 AC: 131638 AN: 152212 Hom.: 57607 Cov.: 33 AF XY: 0.866 AC XY: 64496 AN XY: 74440

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.886

Alfa AF: 0.892 Hom.: 7575

Bravo AF: 0.862

Asia WGS AF: 0.908 AC: 3158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2795421; hg19: chr1-232883135;