9-6325345-G-A

Variant names:

• chr9-6325345-G-A
• rs10491835
• ENST00000722750.1:n.102+2856C>T

Variant summary

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

The ENST00000722750.1(ENSG00000294323):​n.102+2856C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,112 control chromosomes in the GnomAD database, including 2,135 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 0.15 (2135 hom., cov: 32)
• Consequence: ENSG00000294323 ENST00000722750.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 3 publications found

Genes affected

ENSG00000294323 (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 (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722750.1. 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
	ENSG00000294323	ENST00000722750.1		n.102+2856C>T		intron	N/A
	ENSG00000294323	ENST00000722751.1		n.103+2856C>T		intron	N/A
	ENSG00000294323	ENST00000722752.1		n.96+2856C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22575 AN: 151994 Hom.: 2133 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.148 AC: 22578 AN: 152112 Hom.: 2135 Cov.: 32 AF XY: 0.151 AC XY: 11242 AN XY: 74364

African (AFR) AF: 0.0566 AC: 2351 AN: 41532

American (AMR) AF: 0.236 AC: 3602 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 375 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1075 AN: 5186

South Asian (SAS) AF: 0.213 AC: 1027 AN: 4814

European-Finnish (FIN) AF: 0.168 AC: 1770 AN: 10544

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11917 AN: 67966

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.171 Hom.: 1430

Bravo AF: 0.152

Asia WGS AF: 0.180 AC: 625 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.16
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10491835; hg19: chr9-6325345; COSMIC: COSV58828973;