9-29568688-T-C

Variant names:

• chr9-29568688-T-C
• rs10491678

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 0.445 in 151,772 control chromosomes in the GnomAD database, including 15,887 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 0.44 (15887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67444 AN: 151652 Hom.: 15867 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.445 AC: 67522 AN: 151772 Hom.: 15887 Cov.: 32 AF XY: 0.448 AC XY: 33195 AN XY: 74136

African (AFR) AF: 0.563 AC: 23320 AN: 41416

American (AMR) AF: 0.444 AC: 6749 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.788 AC: 4051 AN: 5142

South Asian (SAS) AF: 0.471 AC: 2272 AN: 4820

European-Finnish (FIN) AF: 0.394 AC: 4160 AN: 10560

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24507 AN: 67840

Other (OTH) AF: 0.418 AC: 883 AN: 2110

Alfa AF: 0.388 Hom.: 21033

Bravo AF: 0.455

Asia WGS AF: 0.601 AC: 2090 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.66
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10491678; hg19: chr9-29568686;