9-85297756-C-T

Variant names:

• chr9-85297756-C-T
• rs2769605

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 0.439 in 152,102 control chromosomes in the GnomAD database, including 16,667 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 0.44 (16667 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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: 0.439 AC: 66748 AN: 151984 Hom.: 16674 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.439 AC: 66751 AN: 152102 Hom.: 16667 Cov.: 33 AF XY: 0.439 AC XY: 32633 AN XY: 74352

African (AFR) AF: 0.214 AC: 8873 AN: 41490

American (AMR) AF: 0.423 AC: 6467 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1862 AN: 3470

East Asian (EAS) AF: 0.194 AC: 1007 AN: 5182

South Asian (SAS) AF: 0.579 AC: 2788 AN: 4812

European-Finnish (FIN) AF: 0.538 AC: 5690 AN: 10574

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38393 AN: 67980

Other (OTH) AF: 0.474 AC: 999 AN: 2108

Alfa AF: 0.496 Hom.: 35183

Bravo AF: 0.412

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2769605; hg19: chr9-87912671;