rs2769612

Positions:

• chr9-85294824-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;