chr9-13401549-A-G

Variant names:

• chr9-13401549-A-G
• rs17190837
• ENST00000664575.2:n.100+15321A>G

Variant summary

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

The ENST00000664575.2(ENSG00000226197):​n.100+15321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,222 control chromosomes in the GnomAD database, including 995 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 0.11 (995 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000664575.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.387
• Publications: 1 publications found

Genes affected

ENSG00000226197 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664575.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226197	ENST00000664575.2		n.100+15321A>G		intron	N/A
	ENSG00000226197	ENST00000840204.1		n.278+22378A>G		intron	N/A
	ENSG00000226197	ENST00000840206.1		n.96+15321A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15991 AN: 152104 Hom.: 995 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0478

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.105 AC: 16001 AN: 152222 Hom.: 995 Cov.: 32 AF XY: 0.102 AC XY: 7619 AN XY: 74418

African (AFR) AF: 0.0520 AC: 2160 AN: 41564

American (AMR) AF: 0.103 AC: 1578 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 526 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5176

South Asian (SAS) AF: 0.0493 AC: 238 AN: 4830

European-Finnish (FIN) AF: 0.121 AC: 1277 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9594 AN: 68006

Other (OTH) AF: 0.120 AC: 254 AN: 2108

Alfa AF: 0.109 Hom.: 143

Bravo AF: 0.104

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.56
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs17190837; hg19: chr9-13401548;