9-26608594-T-C

Variant names:

• chr9-26608594-T-C
• rs10967436

Variant summary

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

The variant allele was found at a frequency of 0.272 in 142,650 control chromosomes in the GnomAD database, including 4,962 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 0.27 (4962 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.272 AC: 38795 AN: 142536 Hom.: 4956 Cov.: 29

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.272 AC: 38830 AN: 142650 Hom.: 4962 Cov.: 29 AF XY: 0.278 AC XY: 19262 AN XY: 69246

African (AFR) AF: 0.235 AC: 9173 AN: 39088

American (AMR) AF: 0.351 AC: 4845 AN: 13808

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 837 AN: 3318

East Asian (EAS) AF: 0.235 AC: 1088 AN: 4622

South Asian (SAS) AF: 0.259 AC: 1062 AN: 4096

European-Finnish (FIN) AF: 0.341 AC: 3288 AN: 9632

Middle Eastern (MID) AF: 0.239 AC: 67 AN: 280

European-Non Finnish (NFE) AF: 0.272 AC: 17674 AN: 64998

Other (OTH) AF: 0.291 AC: 562 AN: 1928

Alfa AF: 0.161 Hom.: 335

Bravo AF: 0.255

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs10967436; hg19: chr9-26608592;