ENST00000418395.1:n.182-63086A>C

Variant names:

• chr7-91403759-A-C
• rs6951656
• ENST00000418395.1:n.182-63086A>C

Variant summary

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

The ENST00000418395.1(LINC02932):​n.182-63086A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,292 control chromosomes in the GnomAD database, including 15,144 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 0.41 (15144 hom., cov: 31)
• 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=-0.87).
• 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.244-63086A>C		intron_variant	Intron 3 of 6
LINC02932	NR_183367.1	n.244-63086A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02932	ENST00000418395.1	n.182-63086A>C		intron_variant	Intron 2 of 5	3
ENSG00000223665	ENST00000456952.1	n.113-22892T>G		intron_variant	Intron 1 of 1	3
ENSG00000223665	ENST00000718158.1	n.323-22892T>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.410 AC: 61960 AN: 151168 Hom.: 15144 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.410 AC: 61956 AN: 151292 Hom.: 15144 Cov.: 31 AF XY: 0.407 AC XY: 30027 AN XY: 73856

African (AFR) AF: 0.168 AC: 6971 AN: 41466

American (AMR) AF: 0.375 AC: 5600 AN: 14916

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1809 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1190 AN: 4858

South Asian (SAS) AF: 0.348 AC: 1670 AN: 4804

European-Finnish (FIN) AF: 0.548 AC: 5789 AN: 10556

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37404 AN: 67914

Other (OTH) AF: 0.440 AC: 925 AN: 2104

Alfa AF: 0.501 Hom.: 20941

Bravo AF: 0.388

Asia WGS AF: 0.263 AC: 907 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs6951656; hg19: chr7-91033074;