5-74382559-T-A

Position:

• chr5-74382559-T-A

Variant summary

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

The NR_126354.1(LINC01331):​n.423-13038A>T 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 0.811 in 152,220 control chromosomes in the GnomAD database, including 50,235 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 0.81 (50235 hom., cov: 33)
• Consequence: LINC01331 NR_126354.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01331	NR_126354.1	n.423-13038A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01331	ENST00000663633.1	n.156-13038A>T		intron_variant, non_coding_transcript_variant
LINC01331	ENST00000507781.1	n.423-13038A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123312 AN: 152102 Hom.: 50219 Cov.: 33

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.811 AC: 123380 AN: 152220 Hom.: 50235 Cov.: 33 AF XY: 0.808 AC XY: 60146 AN XY: 74420

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.843

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.807

Alfa AF: 0.823 Hom.: 6413

Bravo AF: 0.803

Asia WGS AF: 0.708 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs586853; hg19: chr5-73678384;