9-24605823-A-G

Variant names:

• chr9-24605823-A-G
• rs1162608
• ENST00000826532.2:n.488+15372A>G

Variant summary

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

The ENST00000826532.2(ENSG00000269957):​n.488+15372A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,784 control chromosomes in the GnomAD database, including 3,872 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 0.21 (3872 hom., cov: 32)
• Consequence: ENSG00000269957 ENST00000826532.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543
• Publications: 3 publications found

Genes affected

ENSG00000269957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826532.2. 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
	ENSG00000269957	ENST00000826532.2		n.488+15372A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32516 AN: 151666 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.214 AC: 32522 AN: 151784 Hom.: 3872 Cov.: 32 AF XY: 0.212 AC XY: 15768 AN XY: 74216

African (AFR) AF: 0.112 AC: 4644 AN: 41514

American (AMR) AF: 0.254 AC: 3863 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1065 AN: 3470

East Asian (EAS) AF: 0.124 AC: 640 AN: 5176

South Asian (SAS) AF: 0.164 AC: 791 AN: 4816

European-Finnish (FIN) AF: 0.233 AC: 2467 AN: 10600

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.269 AC: 18228 AN: 67706

Other (OTH) AF: 0.256 AC: 539 AN: 2104

Alfa AF: 0.255 Hom.: 8777

Bravo AF: 0.214

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.59
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1162608; hg19: chr9-24605821;