rs3852494

chr10-91051639-G-A

Variant summary

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

The NR_047467.2(LINC00502):n.359+3610G>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 0.159 in 152,212 control chromosomes in the GnomAD database, including 3,567 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 0.16 (3567 hom., cov: 32)
• Consequence: LINC00502 NR_047467.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

Genes affected

LINC00502 (HGNC:43442): (long intergenic non-protein coding RNA 502)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00502	NR_047467.2	n.359+3610G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00502	ENST00000423621.2	n.814+3610G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24180 AN: 152094 Hom.: 3542 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0109

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.159 AC: 24245 AN: 152212 Hom.: 3567 Cov.: 32 AF XY: 0.154 AC XY: 11476 AN XY: 74430

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.0705

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.0485

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.0780

Gnomad4 OTH AF: 0.118

Alfa AF: 0.123 Hom.: 254

Bravo AF: 0.169

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	8.3
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: rs3852494; hg19: chr10-92811396;