7-91417678-T-C

Variant names:

• chr7-91417678-T-C
• rs13239130
• ENST00000418395.1:n.182-49167T>C

Variant summary

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

The ENST00000418395.1(LINC02932):​n.182-49167T>C variant causes a intron 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 ENST00000418395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000418395.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02932	NR_183366.1		n.244-49167T>C		intron	N/A
	LINC02932	NR_183367.1		n.244-49167T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02932	ENST00000418395.1	TSL:3	n.182-49167T>C		intron	N/A
	ENSG00000223665	ENST00000456952.1	TSL:3	n.113-36811A>G		intron	N/A
	ENSG00000223665	ENST00000718158.1		n.323-36811A>G		intron	N/A

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

African (AFR) AF: 0.193 AC: 8009 AN: 41490

American (AMR) AF: 0.526 AC: 8011 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2225 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2067 AN: 5142

South Asian (SAS) AF: 0.510 AC: 2446 AN: 4800

European-Finnish (FIN) AF: 0.667 AC: 7052 AN: 10578

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45568 AN: 67910

Other (OTH) AF: 0.550 AC: 1162 AN: 2114

Alfa AF: 0.557 Hom.: 4535

Bravo AF: 0.487

Asia WGS AF: 0.432 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.60
PhyloP100		0.015

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13239130;

hg19: chr7-91046993;