chr9-26524418-T-C

Variant names:

• chr9-26524418-T-C
• rs4111166

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.478 in 151,970 control chromosomes in the GnomAD database, including 17,686 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 0.48 (17686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72546 AN: 151852 Hom.: 17658 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.478 AC: 72626 AN: 151970 Hom.: 17686 Cov.: 32 AF XY: 0.474 AC XY: 35227 AN XY: 74248

African (AFR) AF: 0.483 AC: 20039 AN: 41474

American (AMR) AF: 0.429 AC: 6537 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3472

East Asian (EAS) AF: 0.127 AC: 657 AN: 5164

South Asian (SAS) AF: 0.562 AC: 2702 AN: 4806

European-Finnish (FIN) AF: 0.482 AC: 5087 AN: 10554

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34364 AN: 67932

Other (OTH) AF: 0.444 AC: 938 AN: 2112

Alfa AF: 0.492 Hom.: 57937

Bravo AF: 0.467

Asia WGS AF: 0.395 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	18
DANN	Benign	0.86
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs4111166; hg19: chr9-26524416; COSMIC: COSV69455209;