rs2140005

Variant names:

• chr15-23764141-G-A
• rs2140005
• ENST00000658937.1:n.459+6568G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658937.1(ENSG00000286973):​n.459+6568G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,046 control chromosomes in the GnomAD database, including 13,978 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 0.40 (13978 hom., cov: 32)
• Consequence: ENSG00000286973 ENST00000658937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 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
ENSG00000286973	ENST00000658937.1	n.459+6568G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60918 AN: 151928 Hom.: 13975 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.401 AC: 60939 AN: 152046 Hom.: 13978 Cov.: 32 AF XY: 0.407 AC XY: 30245 AN XY: 74316

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.448

Alfa AF: 0.425 Hom.: 2885

Bravo AF: 0.390

Asia WGS AF: 0.548 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.068
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2140005; hg19: chr15-24009288;