chr9-85294824-T-C

Variant names:

• chr9-85294824-T-C
• rs2769612

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 0.439 in 151,922 control chromosomes in the GnomAD database, including 16,642 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 (16642 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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: 0.439 AC: 66681 AN: 151804 Hom.: 16649 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.634

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: 66682 AN: 151922 Hom.: 16642 Cov.: 31 AF XY: 0.439 AC XY: 32597 AN XY: 74250

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.474

Alfa AF: 0.542 Hom.: 46092

Bravo AF: 0.412

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2769612; hg19: chr9-87909739;