chr9-108805343-C-T

Variant names:

• chr9-108805343-C-T
• rs957235

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 0.184 in 142,638 control chromosomes in the GnomAD database, including 2,386 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 0.18 (2386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 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: 0.183 AC: 26129 AN: 142520 Hom.: 2373 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0606

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.192

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.184 AC: 26182 AN: 142638 Hom.: 2386 Cov.: 32 AF XY: 0.183 AC XY: 12745 AN XY: 69604

African (AFR) AF: 0.225 AC: 8182 AN: 36330

American (AMR) AF: 0.249 AC: 3701 AN: 14862

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 399 AN: 3394

East Asian (EAS) AF: 0.162 AC: 793 AN: 4898

South Asian (SAS) AF: 0.229 AC: 1047 AN: 4564

European-Finnish (FIN) AF: 0.0948 AC: 925 AN: 9762

Middle Eastern (MID) AF: 0.203 AC: 59 AN: 290

European-Non Finnish (NFE) AF: 0.162 AC: 10623 AN: 65686

Other (OTH) AF: 0.202 AC: 400 AN: 1978

Alfa AF: 0.160 Hom.: 1664

Bravo AF: 0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs957235; hg19: chr9-111567623;