9-32755030-C-T

Variant names:

• chr9-32755030-C-T
• rs10758161
• ENST00000730514.1:n.164+6028G>A

Variant summary

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

The ENST00000730514.1(ENSG00000295509):​n.164+6028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,118 control chromosomes in the GnomAD database, including 50,695 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 0.80 (50695 hom., cov: 31)
• Consequence: ENSG00000295509 ENST00000730514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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

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
	ENSG00000295509	ENST00000730514.1		n.164+6028G>A		intron	N/A
	ENSG00000295509	ENST00000730515.1		n.162+6028G>A		intron	N/A
	ENSG00000295509	ENST00000730516.1		n.158+6028G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121215 AN: 152000 Hom.: 50687 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.797 AC: 121249 AN: 152118 Hom.: 50695 Cov.: 31 AF XY: 0.802 AC XY: 59631 AN XY: 74356

African (AFR) AF: 0.512 AC: 21223 AN: 41430

American (AMR) AF: 0.885 AC: 13539 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3159 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4789 AN: 5168

South Asian (SAS) AF: 0.884 AC: 4259 AN: 4818

European-Finnish (FIN) AF: 0.926 AC: 9822 AN: 10602

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61573 AN: 68012

Other (OTH) AF: 0.832 AC: 1755 AN: 2110

Alfa AF: 0.875 Hom.: 257133

Bravo AF: 0.783

Asia WGS AF: 0.870 AC: 3028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.78
DANN	Benign	0.44
PhyloP100		-0.46

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: rs10758161;

hg19: chr9-32755028;