15-93289986-G-A

Variant names:

• chr15-93289986-G-A
• rs7174649
• ENST00000667030.1:n.236+30749G>A

Variant summary

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

The ENST00000667030.1(ENSG00000257060):​n.236+30749G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,208 control chromosomes in the GnomAD database, including 1,226 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 0.12 (1226 hom., cov: 33)
• Consequence: ENSG00000257060 ENST00000667030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000667030.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257060	ENST00000667030.1		n.236+30749G>A		intron	N/A
	ENSG00000257060	ENST00000791023.1		n.533+58134G>A		intron	N/A
	ENSG00000257060	ENST00000791024.1		n.91-32237G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18431 AN: 152090 Hom.: 1228 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.121 AC: 18423 AN: 152208 Hom.: 1226 Cov.: 33 AF XY: 0.119 AC XY: 8831 AN XY: 74410

African (AFR) AF: 0.137 AC: 5691 AN: 41524

American (AMR) AF: 0.0953 AC: 1456 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0744 AC: 359 AN: 4828

European-Finnish (FIN) AF: 0.104 AC: 1096 AN: 10586

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8969 AN: 68006

Other (OTH) AF: 0.134 AC: 284 AN: 2114

Alfa AF: 0.121 Hom.: 465

Bravo AF: 0.125

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7174649; hg19: chr15-93833215;