chr9-34167735-T-G

Variant names:

• chr9-34167735-T-G
• rs7018487

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 0.343 in 152,120 control chromosomes in the GnomAD database, including 9,769 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 0.34 (9769 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 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: 0.343 AC: 52090 AN: 152004 Hom.: 9757 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.343 AC: 52140 AN: 152120 Hom.: 9769 Cov.: 32 AF XY: 0.351 AC XY: 26101 AN XY: 74350

African (AFR) AF: 0.259 AC: 10755 AN: 41512

American (AMR) AF: 0.397 AC: 6070 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1207 AN: 3472

East Asian (EAS) AF: 0.736 AC: 3812 AN: 5178

South Asian (SAS) AF: 0.530 AC: 2555 AN: 4818

European-Finnish (FIN) AF: 0.343 AC: 3628 AN: 10572

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22898 AN: 67976

Other (OTH) AF: 0.367 AC: 774 AN: 2110

Alfa AF: 0.338 Hom.: 11200

Bravo AF: 0.343

Asia WGS AF: 0.590 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.89
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs7018487; hg19: chr9-34167733; COSMIC: COSV63496075;