9-25425162-T-G

Variant names:

• chr9-25425162-T-G
• rs10966900
• ENST00000732866.1:n.119-2465A>C

Variant summary

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

The ENST00000732866.1(ENSG00000295812):​n.119-2465A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,084 control chromosomes in the GnomAD database, including 3,340 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 (3340 hom., cov: 32)
• Consequence: ENSG00000295812 ENST00000732866.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835
• Publications: 2 publications found

Genes affected

ENSG00000295812 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000732866.1. 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
	ENSG00000295812	ENST00000732866.1		n.119-2465A>C		intron	N/A
	ENSG00000295812	ENST00000732867.1		n.108-2465A>C		intron	N/A
	ENSG00000295812	ENST00000732868.1		n.96-5353A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30778 AN: 151966 Hom.: 3334 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.203 AC: 30809 AN: 152084 Hom.: 3340 Cov.: 32 AF XY: 0.205 AC XY: 15245 AN XY: 74360

African (AFR) AF: 0.239 AC: 9908 AN: 41468

American (AMR) AF: 0.172 AC: 2631 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2002 AN: 5154

South Asian (SAS) AF: 0.236 AC: 1137 AN: 4816

European-Finnish (FIN) AF: 0.205 AC: 2175 AN: 10586

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11782 AN: 67990

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.179 Hom.: 1697

Bravo AF: 0.203

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.76
PhyloP100		-0.83

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: rs10966900;

hg19: chr9-25425160;

COSMIC: COSV60344913;