13-40366650-C-T

Variant names:

• chr13-40366650-C-T
• rs1041210
• ENST00000636621.1:n.71-16348G>A

Variant summary

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

The ENST00000636621.1(LINC00598):​n.71-16348G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,144 control chromosomes in the GnomAD database, including 937 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 0.10 (937 hom., cov: 32)
• Consequence: LINC00598 ENST00000636621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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.662-16348G>A		intron	N/A
	LINC00598	NR_024507.3		n.802-16348G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000636621.1	TSL:1	n.71-16348G>A		intron	N/A
	LINC00598	ENST00000400432.4	TSL:5	n.117-16348G>A		intron	N/A
	LINC00598	ENST00000636192.2	TSL:5	n.178-16348G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15443 AN: 152026 Hom.: 929 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0709

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.102 AC: 15481 AN: 152144 Hom.: 937 Cov.: 32 AF XY: 0.104 AC XY: 7731 AN XY: 74376

African (AFR) AF: 0.132 AC: 5458 AN: 41466

American (AMR) AF: 0.158 AC: 2417 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5184

South Asian (SAS) AF: 0.0714 AC: 344 AN: 4820

European-Finnish (FIN) AF: 0.0779 AC: 825 AN: 10588

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4807 AN: 68004

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0732 Hom.: 516

Bravo AF: 0.114

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.76
PhyloP100		0.11

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: rs1041210;

hg19: chr13-40940787;