ENST00000418395.1:n.182-21912A>G

Variant names:

• chr7-91444933-A-G
• rs4504558
• ENST00000418395.1:n.182-21912A>G

Variant summary

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

The ENST00000418395.1(LINC02932):​n.182-21912A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,930 control chromosomes in the GnomAD database, including 14,714 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 (14714 hom., cov: 30)
• Consequence: LINC02932 ENST00000418395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.546 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02932	NR_183366.1		n.244-21912A>G		intron	N/A
	LINC02932	NR_183367.1		n.244-21912A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02932	ENST00000418395.1	TSL:3	n.182-21912A>G		intron	N/A
	ENSG00000223665	ENST00000456952.1	TSL:3	n.113-64066T>C		intron	N/A
	ENSG00000223665	ENST00000718158.1		n.323-64066T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61652 AN: 151812 Hom.: 14718 Cov.: 30

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.406 AC: 61641 AN: 151930 Hom.: 14714 Cov.: 30 AF XY: 0.402 AC XY: 29854 AN XY: 74256

African (AFR) AF: 0.166 AC: 6899 AN: 41468

American (AMR) AF: 0.356 AC: 5431 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1821 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1088 AN: 5154

South Asian (SAS) AF: 0.349 AC: 1679 AN: 4810

European-Finnish (FIN) AF: 0.548 AC: 5776 AN: 10544

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37434 AN: 67918

Other (OTH) AF: 0.435 AC: 916 AN: 2104

Alfa AF: 0.501 Hom.: 10232

Bravo AF: 0.383

Asia WGS AF: 0.248 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4504558; hg19: chr7-91074248;