13-40374014-C-T

Variant names:

• chr13-40374014-C-T
• rs913246
• ENST00000636621.1:n.71-23712G>A

Variant summary

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

The ENST00000636621.1(LINC00598):​n.71-23712G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,322 control chromosomes in the GnomAD database, including 70,875 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 0.96 (70875 hom., cov: 32)
• Consequence: LINC00598 ENST00000636621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000636621.1. 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
	LINC00598	NR_024506.2		n.662-23712G>A		intron	N/A
	LINC00598	NR_024507.3		n.802-23712G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000636621.1	TSL:1	n.71-23712G>A		intron	N/A
	LINC00598	ENST00000400432.4	TSL:5	n.117-23712G>A		intron	N/A
	LINC00598	ENST00000636192.2	TSL:5	n.178-23712G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146807 AN: 152204 Hom.: 70821 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.965 AC: 146920 AN: 152322 Hom.: 70875 Cov.: 32 AF XY: 0.963 AC XY: 71702 AN XY: 74474

African (AFR) AF: 0.945 AC: 39257 AN: 41556

American (AMR) AF: 0.976 AC: 14944 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.970 AC: 3369 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5120 AN: 5182

South Asian (SAS) AF: 0.936 AC: 4519 AN: 4826

European-Finnish (FIN) AF: 0.938 AC: 9951 AN: 10614

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66583 AN: 68040

Other (OTH) AF: 0.961 AC: 2034 AN: 2116

Alfa AF: 0.973 Hom.: 105006

Bravo AF: 0.967

Asia WGS AF: 0.956 AC: 3327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.17
PhyloP100		-3.7

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: rs913246;

hg19: chr13-40948151;