rs9302364

Variant names:

• chr15-93156598-A-G
• rs9302364
• ENST00000711606.1:n.513-13845A>G

Variant summary

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

The ENST00000711606.1(ENSG00000257060):​n.513-13845A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,136 control chromosomes in the GnomAD database, including 3,098 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 0.20 (3098 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000711606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000711606.1. 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
	ENSG00000257060	ENST00000711606.1		n.513-13845A>G		intron	N/A
	ENSG00000257060	ENST00000791023.1		n.204-13845A>G		intron	N/A
	ENSG00000257060	ENST00000791051.1		n.417-13845A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30098 AN: 152016 Hom.: 3099 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.198 AC: 30114 AN: 152136 Hom.: 3098 Cov.: 32 AF XY: 0.199 AC XY: 14820 AN XY: 74384

African (AFR) AF: 0.191 AC: 7936 AN: 41504

American (AMR) AF: 0.178 AC: 2720 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3468

East Asian (EAS) AF: 0.173 AC: 897 AN: 5184

South Asian (SAS) AF: 0.212 AC: 1022 AN: 4818

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10576

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13795 AN: 67988

Other (OTH) AF: 0.172 AC: 363 AN: 2106

Alfa AF: 0.197 Hom.: 9255

Bravo AF: 0.193

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.8
DANN	Benign	0.80
PhyloP100		0.57

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9302364;

hg19: chr15-93699827;