chr9-85300394-C-T

Variant names:

• chr9-85300394-C-T
• rs2769600

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 0.44 in 151,924 control chromosomes in the GnomAD database, including 16,660 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 (16660 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.562 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: 0.440 AC: 66776 AN: 151806 Hom.: 16667 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.440 AC: 66777 AN: 151924 Hom.: 16660 Cov.: 31 AF XY: 0.440 AC XY: 32643 AN XY: 74232

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.477

Alfa AF: 0.527 Hom.: 10675

Bravo AF: 0.412

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2769600; hg19: chr9-87915309;