rs2140005

chr15-23764141-G-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, non coding transcript 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: ENST00000658937.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658937.1	n.459+6568G>A		intron_variant, non_coding_transcript_variant

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;