7-91417678-T-C

Variant summary

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

The NR_183366.1(LINC02932):n.244-49167T>C 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 0.509 in 151,938 control chromosomes in the GnomAD database, including 22,882 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 0.51 (22882 hom., cov: 32)
• Consequence: LINC02932 NR_183366.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02932	NR_183366.1	n.244-49167T>C		intron_variant, non_coding_transcript_variant
LINC02932	NR_183367.1	n.244-49167T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02932	ENST00000418395.1	n.182-49167T>C		intron_variant, non_coding_transcript_variant		3
	ENST00000456952.1	n.113-36811A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77265 AN: 151820 Hom.: 22885 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.509 AC: 77274 AN: 151938 Hom.: 22882 Cov.: 32 AF XY: 0.509 AC XY: 37786 AN XY: 74264

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.550

Alfa AF: 0.567 Hom.: 4516

Bravo AF: 0.487

Asia WGS AF: 0.432 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.0
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13239130; hg19: chr7-91046993;