15-95789632-A-G

Variant names:

• chr15-95789632-A-G
• rs2567426
• ENST00000612595.2:n.284-35557A>G

Variant summary

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

The ENST00000656202.1(ENSG00000275016):​n.235-35557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 151,910 control chromosomes in the GnomAD database, including 38,060 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 0.70 (38060 hom., cov: 31)
• Consequence: ENSG00000275016 ENST00000656202.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 8 publications found

Genes affected

ENSG00000275016 (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 = 0.813 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656202.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275016	ENST00000612595.2	TSL:5	n.284-35557A>G		intron	N/A
	ENSG00000275016	ENST00000616588.4	TSL:5	n.251-20447A>G		intron	N/A
	ENSG00000275016	ENST00000656202.1		n.235-35557A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106667 AN: 151792 Hom.: 38004 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.703 AC: 106780 AN: 151910 Hom.: 38060 Cov.: 31 AF XY: 0.699 AC XY: 51915 AN XY: 74260

African (AFR) AF: 0.820 AC: 33989 AN: 41460

American (AMR) AF: 0.700 AC: 10674 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2301 AN: 3470

East Asian (EAS) AF: 0.824 AC: 4258 AN: 5170

South Asian (SAS) AF: 0.617 AC: 2975 AN: 4820

European-Finnish (FIN) AF: 0.574 AC: 6040 AN: 10530

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44201 AN: 67894

Other (OTH) AF: 0.713 AC: 1501 AN: 2106

Alfa AF: 0.670 Hom.: 107707

Bravo AF: 0.722

Asia WGS AF: 0.682 AC: 2366 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.038
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2567426; hg19: chr15-96332861;