rs7034462

Variant names:

• chr9-99095919-C-T
• rs7034462

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 0.0801 in 152,082 control chromosomes in the GnomAD database, including 570 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 0.080 (570 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.717
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0927 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: 0.0801 AC: 12165 AN: 151964 Hom.: 572 Cov.: 33

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.0427

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0801 AC: 12177 AN: 152082 Hom.: 570 Cov.: 33 AF XY: 0.0807 AC XY: 6000 AN XY: 74326

African (AFR) AF: 0.0612 AC: 2540 AN: 41486

American (AMR) AF: 0.0594 AC: 908 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5182

South Asian (SAS) AF: 0.0429 AC: 207 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1380 AN: 10568

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6430 AN: 67968

Other (OTH) AF: 0.0809 AC: 170 AN: 2102

Alfa AF: 0.0886 Hom.: 330

Bravo AF: 0.0750

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.1
DANN	Benign	0.69
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs7034462; hg19: chr9-101858201;