13-74368758-G-A

Variant names:

• chr13-74368758-G-A
• rs9318258
• ENST00000653841.1:n.211+3671G>A

Variant summary

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

The NR_187793.1(LOC105370259):​n.389+3671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,742 control chromosomes in the GnomAD database, including 7,112 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 0.29 (7112 hom., cov: 31)
• Consequence: LOC105370259 NR_187793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 5 publications found

Genes affected

LINC00402 (HGNC:42732): (long intergenic non-protein coding RNA 402)

LOC105370259 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_187793.1. 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
	LOC105370259	NR_187793.1		n.389+3671G>A		intron	N/A
	LOC105370259	NR_187794.1		n.389+3671G>A		intron	N/A
	LOC105370259	NR_187795.1		n.451+3671G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00402	ENST00000653841.1		n.211+3671G>A		intron	N/A
	LINC00402	ENST00000653992.1		n.275+3671G>A		intron	N/A
	LINC00402	ENST00000654479.1		n.430+3671G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43808 AN: 151624 Hom.: 7093 Cov.: 31

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.289 AC: 43871 AN: 151742 Hom.: 7112 Cov.: 31 AF XY: 0.289 AC XY: 21431 AN XY: 74134

African (AFR) AF: 0.441 AC: 18256 AN: 41374

American (AMR) AF: 0.329 AC: 5005 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1142 AN: 3468

East Asian (EAS) AF: 0.162 AC: 832 AN: 5142

South Asian (SAS) AF: 0.267 AC: 1281 AN: 4802

European-Finnish (FIN) AF: 0.218 AC: 2293 AN: 10510

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14013 AN: 67898

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.241 Hom.: 8327

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.77
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs9318258; hg19: chr13-74942895;