9-32717015-T-C

Variant names:

• chr9-32717015-T-C
• rs1328994
• ENST00000730514.1:n.165-11644A>G

Variant summary

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

The ENST00000730514.1(ENSG00000295509):​n.165-11644A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,952 control chromosomes in the GnomAD database, including 26,352 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 0.58 (26352 hom., cov: 31)
• Consequence: ENSG00000295509 ENST00000730514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 6 publications found

Genes affected

ENSG00000295509 (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 (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730514.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295509	ENST00000730514.1		n.165-11644A>G		intron	N/A
	ENSG00000295509	ENST00000730515.1		n.232-11644A>G		intron	N/A
	ENSG00000295509	ENST00000730516.1		n.228-11644A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88501 AN: 151834 Hom.: 26325 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.583 AC: 88572 AN: 151952 Hom.: 26352 Cov.: 31 AF XY: 0.575 AC XY: 42713 AN XY: 74256

African (AFR) AF: 0.700 AC: 28990 AN: 41416

American (AMR) AF: 0.518 AC: 7910 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2116 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4812

European-Finnish (FIN) AF: 0.496 AC: 5220 AN: 10528

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38363 AN: 67966

Other (OTH) AF: 0.566 AC: 1196 AN: 2112

Alfa AF: 0.569 Hom.: 97825

Bravo AF: 0.588

Asia WGS AF: 0.454 AC: 1583 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	10
DANN	Benign	0.75
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs1328994; hg19: chr9-32717013;