rs2038946

Variant names:

• chr13-74547065-A-G
• rs2038946
• ENST00000715466.1:n.147+3164A>G

Variant summary

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

The ENST00000715466.1(LINC00402):​n.147+3164A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,924 control chromosomes in the GnomAD database, including 15,708 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 0.43 (15708 hom., cov: 32)
• Consequence: LINC00402 ENST00000715466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 2 publications found

Genes affected

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

ENSG00000307743 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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
LINC00402	ENST00000715466.1	n.147+3164A>G		intron_variant	Intron 2 of 6
ENSG00000307743	ENST00000828401.1	n.83-42753T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65331 AN: 151806 Hom.: 15702 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.430 AC: 65353 AN: 151924 Hom.: 15708 Cov.: 32 AF XY: 0.430 AC XY: 31953 AN XY: 74250

African (AFR) AF: 0.205 AC: 8523 AN: 41502

American (AMR) AF: 0.418 AC: 6380 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1521 AN: 3466

East Asian (EAS) AF: 0.751 AC: 3882 AN: 5168

South Asian (SAS) AF: 0.534 AC: 2567 AN: 4806

European-Finnish (FIN) AF: 0.492 AC: 5152 AN: 10478

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35962 AN: 67920

Other (OTH) AF: 0.426 AC: 898 AN: 2110

Alfa AF: 0.513 Hom.: 11925

Bravo AF: 0.415

Asia WGS AF: 0.576 AC: 1975 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.35
DANN	Benign	0.82
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs2038946; hg19: chr13-75121202;