rs294993

Positions:

• chr5-74435916-A-G

Variant summary

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

The NR_126354.1(LINC01331):​n.422+40422T>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 0.781 in 151,982 control chromosomes in the GnomAD database, including 46,526 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 0.78 (46526 hom., cov: 32)
• Consequence: LINC01331 NR_126354.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

LINC01331 (HGNC:50538): (long intergenic non-protein coding RNA 1331)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01331	NR_126354.1	n.422+40422T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01331	ENST00000663633.1	n.156-66395T>C		intron_variant, non_coding_transcript_variant
LINC01331	ENST00000507781.1	n.422+40422T>C		intron_variant, non_coding_transcript_variant		4
LINC01331	ENST00000657957.1	n.229+40422T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118637 AN: 151862 Hom.: 46497 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.781 AC: 118720 AN: 151982 Hom.: 46526 Cov.: 32 AF XY: 0.776 AC XY: 57659 AN XY: 74290

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.804

Alfa AF: 0.788 Hom.: 5878

Bravo AF: 0.783

Asia WGS AF: 0.754 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.35
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs294993; hg19: chr5-73731741;