rs13246435

Positions:

• chr7-91398500-C-T

Variant summary

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

The NR_183366.1(LINC02932):​n.244-68345C>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 0.418 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 NR_183366.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02932	NR_183366.1	n.244-68345C>T		intron_variant, non_coding_transcript_variant
LINC02932	NR_183367.1	n.244-68345C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02932	ENST00000418395.1	n.182-68345C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000456952.1	n.113-17633G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.443

Alfa AF: 0.520 Hom.: 21894

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13246435; hg19: chr7-91027815;