chr9-13545787-A-C

Variant names:

• chr9-13545787-A-C
• rs10491753
• ENST00000664438.1:n.113-7488A>C

Variant summary

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

The ENST00000664438.1(ENSG00000226197):​n.113-7488A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,290 control chromosomes in the GnomAD database, including 277 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 0.050 (277 hom., cov: 32)
• Consequence: ENSG00000226197 ENST00000664438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0753 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664438.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226197	ENST00000664438.1		n.113-7488A>C		intron	N/A
	ENSG00000226197	ENST00000840201.1		n.289-7488A>C		intron	N/A
	ENSG00000226197	ENST00000840202.1		n.773-7488A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7598 AN: 152172 Hom.: 277 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.0514

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0498 AC: 7591 AN: 152290 Hom.: 277 Cov.: 32 AF XY: 0.0466 AC XY: 3466 AN XY: 74456

African (AFR) AF: 0.0151 AC: 627 AN: 41572

American (AMR) AF: 0.0513 AC: 784 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0389 AC: 135 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5178

South Asian (SAS) AF: 0.0201 AC: 97 AN: 4820

European-Finnish (FIN) AF: 0.0354 AC: 376 AN: 10628

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5240 AN: 68026

Other (OTH) AF: 0.0582 AC: 123 AN: 2112

Alfa AF: 0.0681 Hom.: 204

Bravo AF: 0.0497

Asia WGS AF: 0.0140 AC: 47 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.44
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10491753; hg19: chr9-13545786;