rs2769612

Variant names:

• chr9-85294824-T-C
• rs2769612

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 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.214 AC: 8863 AN: 41446

American (AMR) AF: 0.423 AC: 6459 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1861 AN: 3470

East Asian (EAS) AF: 0.196 AC: 1009 AN: 5150

South Asian (SAS) AF: 0.579 AC: 2786 AN: 4814

European-Finnish (FIN) AF: 0.538 AC: 5674 AN: 10544

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38363 AN: 67926

Other (OTH) AF: 0.474 AC: 996 AN: 2100

Alfa AF: 0.522 Hom.: 90770

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs2769612; hg19: chr9-87909739;