rs2140005

Variant names:

• chr15-23764141-G-A
• rs2140005
• ENST00000658937.2:n.509+6568G>A

Variant summary

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

The ENST00000658937.2(ENSG00000286973):​n.509+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 ENST00000658937.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 3 publications found

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000658937.2	n.509+6568G>A		intron_variant	Intron 1 of 2
ENSG00000286973	ENST00000844005.1	n.471+6568G>A		intron_variant	Intron 1 of 3
ENSG00000286973	ENST00000844006.1	n.471+6568G>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.177 AC: 7356 AN: 41490

American (AMR) AF: 0.449 AC: 6872 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3470

East Asian (EAS) AF: 0.697 AC: 3595 AN: 5160

South Asian (SAS) AF: 0.502 AC: 2414 AN: 4806

European-Finnish (FIN) AF: 0.530 AC: 5579 AN: 10536

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31710 AN: 67976

Other (OTH) AF: 0.448 AC: 944 AN: 2108

Alfa AF: 0.419 Hom.: 2901

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2140005; hg19: chr15-24009288;