rs12415456

Variant names:

• chr10-91033283-A-T
• rs12415456
• ENST00000423621.2:n.38+89A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423621.2(LINC00502):​n.38+89A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,016 control chromosomes in the GnomAD database, including 21,281 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 0.53 (21281 hom., cov: 32)
• Consequence: LINC00502 ENST00000423621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 2 publications found

Genes affected

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

ENSG00000273124 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378430	NR_134319.1	n.29+89A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00502	ENST00000423621.2	n.38+89A>T		intron_variant	Intron 1 of 7	3
ENSG00000273124	ENST00000607979.2	n.151-35455T>A		intron_variant	Intron 1 of 1	6
ENSG00000273124	ENST00000846062.1	n.94+16187T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80136 AN: 151898 Hom.: 21245 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.528 AC: 80239 AN: 152016 Hom.: 21281 Cov.: 32 AF XY: 0.527 AC XY: 39130 AN XY: 74282

African (AFR) AF: 0.551 AC: 22865 AN: 41464

American (AMR) AF: 0.524 AC: 8010 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1647 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2691 AN: 5154

South Asian (SAS) AF: 0.460 AC: 2216 AN: 4822

European-Finnish (FIN) AF: 0.532 AC: 5611 AN: 10554

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35560 AN: 67966

Other (OTH) AF: 0.515 AC: 1085 AN: 2108

Alfa AF: 0.519 Hom.: 2548

Bravo AF: 0.528

Asia WGS AF: 0.463 AC: 1614 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	0.35
DANN	Benign	0.63
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs12415456; hg19: chr10-92793040;