9-24610708-C-G

Variant names:

• chr9-24610708-C-G
• rs1034168
• ENST00000826532.2:n.488+20257C>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+20257C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 151,934 control chromosomes in the GnomAD database, including 800 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 0.091 (800 hom., cov: 32)
• Consequence: ENSG00000269957 ENST00000826532.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 1 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 = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269957	ENST00000826532.2	n.488+20257C>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13853 AN: 151816 Hom.: 797 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0729

Gnomad EAS AF: 0.0339

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0905

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.0913 AC: 13876 AN: 151934 Hom.: 800 Cov.: 32 AF XY: 0.0903 AC XY: 6708 AN XY: 74248

African (AFR) AF: 0.0280 AC: 1161 AN: 41458

American (AMR) AF: 0.116 AC: 1761 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0729 AC: 253 AN: 3470

East Asian (EAS) AF: 0.0341 AC: 176 AN: 5154

South Asian (SAS) AF: 0.126 AC: 605 AN: 4802

European-Finnish (FIN) AF: 0.0905 AC: 956 AN: 10560

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.127 AC: 8600 AN: 67936

Other (OTH) AF: 0.0996 AC: 210 AN: 2108

Alfa AF: 0.0282 Hom.: 25

Bravo AF: 0.0878

Asia WGS AF: 0.115 AC: 400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.34
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1034168; hg19: chr9-24610706;