13-40488891-G-T

Variant names:

• chr13-40488891-G-T
• rs7327461
• ENST00000615137.1:n.143-14796C>A

Variant summary

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

The ENST00000615137.1(LINC00598):​n.143-14796C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 151,938 control chromosomes in the GnomAD database, including 42,734 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 0.74 (42734 hom., cov: 31)
• Consequence: LINC00598 ENST00000615137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 4 publications found

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

ENSG00000288542 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615137.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000615137.1	TSL:3	n.143-14796C>A		intron	N/A
	ENSG00000288542	ENST00000636651.2	TSL:5	n.1460-14796C>A		intron	N/A
	ENSG00000308612	ENST00000835419.1		n.83-2749G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112796 AN: 151820 Hom.: 42722 Cov.: 31

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.743 AC: 112844 AN: 151938 Hom.: 42734 Cov.: 31 AF XY: 0.740 AC XY: 54926 AN XY: 74274

African (AFR) AF: 0.597 AC: 24738 AN: 41428

American (AMR) AF: 0.798 AC: 12206 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2806 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3423 AN: 5134

South Asian (SAS) AF: 0.628 AC: 3020 AN: 4810

European-Finnish (FIN) AF: 0.772 AC: 8136 AN: 10542

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55903 AN: 67950

Other (OTH) AF: 0.776 AC: 1639 AN: 2112

Alfa AF: 0.796 Hom.: 200154

Bravo AF: 0.740

Asia WGS AF: 0.629 AC: 2189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		0.30

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: rs7327461;

hg19: chr13-41063028;