chr9-34550297-C-T

Variant names:

• chr9-34550297-C-T
• rs10814119

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 0.577 in 151,892 control chromosomes in the GnomAD database, including 26,686 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 0.58 (26686 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 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: 0.577 AC: 87587 AN: 151774 Hom.: 26675 Cov.: 31

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.577 AC: 87623 AN: 151892 Hom.: 26686 Cov.: 31 AF XY: 0.576 AC XY: 42753 AN XY: 74220

African (AFR) AF: 0.382 AC: 15803 AN: 41394

American (AMR) AF: 0.568 AC: 8672 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2322 AN: 3468

East Asian (EAS) AF: 0.562 AC: 2886 AN: 5138

South Asian (SAS) AF: 0.598 AC: 2878 AN: 4812

European-Finnish (FIN) AF: 0.627 AC: 6628 AN: 10568

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46502 AN: 67926

Other (OTH) AF: 0.604 AC: 1275 AN: 2112

Alfa AF: 0.643 Hom.: 41961

Bravo AF: 0.562

Asia WGS AF: 0.578 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.57
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs10814119; hg19: chr9-34550295;