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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376017	XR_007061451.1	n.617-11644A>G		intron_variant	Intron 4 of 5
LOC105376017	XR_929559.2	n.617-11644A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295509	ENST00000730514.1	n.165-11644A>G		intron_variant	Intron 1 of 3
ENSG00000295509	ENST00000730515.1	n.232-11644A>G		intron_variant	Intron 2 of 4
ENSG00000295509	ENST00000730516.1	n.228-11644A>G		intron_variant	Intron 2 of 5

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 v4.3

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;