13-74421523-A-G

Variant names:

• chr13-74421523-A-G
• rs17714988
• ENST00000423629.1:n.153+1984A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000423629.1(LINC00402):​n.153+1984A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0564 in 152,322 control chromosomes in the GnomAD database, including 353 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 0.056 (353 hom., cov: 32)
• Consequence: LINC00402 ENST00000423629.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.72
• Publications: 7 publications found

Genes affected

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

LINC00381 (HGNC:42708): (long intergenic non-protein coding RNA 381)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423629.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00381	NR_047005.1		n.153+1984A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00402	ENST00000423629.1	TSL:5	n.153+1984A>G		intron	N/A
	LINC00402	ENST00000649990.1		n.71+2295A>G		intron	N/A
	LINC00402	ENST00000715848.1		n.452-12980A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0565 AC: 8594 AN: 152204 Hom.: 353 Cov.: 32

Gnomad AFR AF: 0.0148

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0527

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0588

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

GnomAD4 genome AF: 0.0564 AC: 8594 AN: 152322 Hom.: 353 Cov.: 32 AF XY: 0.0562 AC XY: 4183 AN XY: 74484

African (AFR) AF: 0.0147 AC: 613 AN: 41596

American (AMR) AF: 0.0473 AC: 724 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0530 AC: 256 AN: 4832

European-Finnish (FIN) AF: 0.0897 AC: 952 AN: 10612

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0825 AC: 5612 AN: 68000

Other (OTH) AF: 0.0577 AC: 122 AN: 2114

Alfa AF: 0.0704 Hom.: 987

Bravo AF: 0.0507

Asia WGS AF: 0.0240 AC: 84 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	19
DANN	Benign	0.86
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs17714988; hg19: chr13-74995660;