chr13-78806681-T-G

Variant names:

• chr13-78806681-T-G
• rs2184180
• ENST00000653901.1:n.112-14189A>C

Variant summary

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

The ENST00000653901.1(LINC00331):​n.112-14189A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,746 control chromosomes in the GnomAD database, including 8,384 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 0.32 (8384 hom., cov: 31)
• Consequence: LINC00331 ENST00000653901.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

Genes affected

LINC00331 (HGNC:42048): (long intergenic non-protein coding RNA 331)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00331	NR_046869.2	n.225-14379A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00331	ENST00000653901.1	n.112-14189A>C		intron_variant	Intron 1 of 4
LINC00331	ENST00000655539.2	n.225-14379A>C		intron_variant	Intron 2 of 5
LINC00331	ENST00000658469.1	n.225-10582A>C		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48442 AN: 151628 Hom.: 8379 Cov.: 31

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.319 AC: 48462 AN: 151746 Hom.: 8384 Cov.: 31 AF XY: 0.320 AC XY: 23755 AN XY: 74150

African (AFR) AF: 0.205 AC: 8502 AN: 41402

American (AMR) AF: 0.446 AC: 6785 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1311 AN: 3460

East Asian (EAS) AF: 0.475 AC: 2450 AN: 5154

South Asian (SAS) AF: 0.354 AC: 1701 AN: 4804

European-Finnish (FIN) AF: 0.268 AC: 2821 AN: 10528

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23785 AN: 67876

Other (OTH) AF: 0.354 AC: 747 AN: 2110

Alfa AF: 0.345 Hom.: 14706

Bravo AF: 0.331

Asia WGS AF: 0.413 AC: 1430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.3
DANN	Benign	0.59
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2184180; hg19: chr13-79380816;