rs13246435

Variant names:

• chr7-91398500-C-T
• rs13246435
• ENST00000418395.1:n.182-68345C>T

Variant summary

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

The ENST00000418395.1(LINC02932):​n.182-68345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,014 control chromosomes in the GnomAD database, including 15,072 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 0.42 (15072 hom., cov: 32)
• Consequence: LINC02932 ENST00000418395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 1 publications found

Genes affected

LINC02932 (HGNC:55875): (long intergenic non-protein coding RNA 2932)

ENSG00000223665 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02932	NR_183366.1	n.244-68345C>T		intron_variant	Intron 3 of 6
LINC02932	NR_183367.1	n.244-68345C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02932	ENST00000418395.1	n.182-68345C>T		intron_variant	Intron 2 of 5	3
ENSG00000223665	ENST00000456952.1	n.113-17633G>A		intron_variant	Intron 1 of 1	3
ENSG00000223665	ENST00000718158.1	n.323-17633G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63514 AN: 151896 Hom.: 15074 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.418 AC: 63510 AN: 152014 Hom.: 15072 Cov.: 32 AF XY: 0.413 AC XY: 30716 AN XY: 74288

African (AFR) AF: 0.212 AC: 8788 AN: 41506

American (AMR) AF: 0.358 AC: 5460 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1813 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5164

South Asian (SAS) AF: 0.345 AC: 1658 AN: 4810

European-Finnish (FIN) AF: 0.547 AC: 5768 AN: 10550

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37408 AN: 67940

Other (OTH) AF: 0.443 AC: 932 AN: 2106

Alfa AF: 0.504 Hom.: 26935

Bravo AF: 0.397

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.67
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs13246435; hg19: chr7-91027815;