rs2567426

Positions:

• chr15-95789632-A-G
• chr15-95789632-A-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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 = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.95789632A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000275016	ENST00000612595.2	n.284-35557A>G		intron_variant		5
ENSG00000275016	ENST00000616588.4	n.251-20447A>G		intron_variant		5
ENSG00000275016	ENST00000656202.1	n.235-35557A>G		intron_variant

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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.713

Alfa AF: 0.658 Hom.: 62373

Bravo AF: 0.722

Asia WGS AF: 0.682 AC: 2366 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2567426; hg19: chr15-96332861;