rs10515180

Positions:

• chr5-74415339-G-A

Variant summary

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

The NR_126354.1(LINC01331):​n.423-45818C>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 0.0142 in 152,164 control chromosomes in the GnomAD database, including 158 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 0.014 (158 hom., cov: 32)
• Consequence: LINC01331 NR_126354.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01331	NR_126354.1	n.423-45818C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01331	ENST00000663633.1	n.156-45818C>T		intron_variant, non_coding_transcript_variant
LINC01331	ENST00000507781.1	n.423-45818C>T		intron_variant, non_coding_transcript_variant		4
LINC01331	ENST00000657957.1	n.230-20804C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0142 AC: 2163 AN: 152046 Hom.: 159 Cov.: 32

Gnomad AFR AF: 0.000991

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00858

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00572

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0142 AC: 2159 AN: 152164 Hom.: 158 Cov.: 32 AF XY: 0.0159 AC XY: 1184 AN XY: 74390

Gnomad4 AFR AF: 0.000988

Gnomad4 AMR AF: 0.00857

Gnomad4 ASJ AF: 0.00951

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.0380

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.00572

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00994 Hom.: 7

Bravo AF: 0.0131

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515180; hg19: chr5-73711164;