chr9-99095919-C-T

Variant names:

• chr9-99095919-C-T
• rs7034462

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0612

Gnomad4 AMR AF: 0.0594

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0429

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.0809

Alfa AF: 0.0880 Hom.: 292

Bravo AF: 0.0750

Asia WGS AF: 0.0390 AC: 136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7034462; hg19: chr9-101858201;