13-30856349-T-C

Variant names:

• chr13-30856349-T-C
• rs1831549
• ENST00000715721.1:n.709-26211T>C

Variant summary

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

The ENST00000715721.1(LINC00398):​n.709-26211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,028 control chromosomes in the GnomAD database, including 35,659 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 0.68 (35659 hom., cov: 31)
• Consequence: LINC00398 ENST00000715721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 6 publications found

Genes affected

LINC00398 (HGNC:42727): (long intergenic non-protein coding RNA 398)

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 (SAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00398	ENST00000715721.1	n.709-26211T>C		intron_variant	Intron 3 of 3
LINC00398	ENST00000799400.1	n.136+25482T>C		intron_variant	Intron 1 of 2
LINC00398	ENST00000799401.1	n.53-922T>C		intron_variant	Intron 1 of 3
LINC00398	ENST00000799402.1	n.127+7958T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103372 AN: 151910 Hom.: 35625 Cov.: 31

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.681 AC: 103463 AN: 152028 Hom.: 35659 Cov.: 31 AF XY: 0.687 AC XY: 51058 AN XY: 74314

African (AFR) AF: 0.580 AC: 24036 AN: 41440

American (AMR) AF: 0.714 AC: 10908 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2324 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3701 AN: 5170

South Asian (SAS) AF: 0.813 AC: 3920 AN: 4820

European-Finnish (FIN) AF: 0.740 AC: 7812 AN: 10554

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48436 AN: 67988

Other (OTH) AF: 0.666 AC: 1403 AN: 2106

Alfa AF: 0.707 Hom.: 21180

Bravo AF: 0.668

Asia WGS AF: 0.756 AC: 2627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.8
DANN	Benign	0.72
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1831549; hg19: chr13-31430486; COSMIC: COSV69345991;