9-79274443-G-C

Variant names:

• chr9-79274443-G-C
• rs2769967

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 0.474 in 152,072 control chromosomes in the GnomAD database, including 17,500 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 0.47 (17500 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 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: 0.474 AC: 72019 AN: 151954 Hom.: 17469 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.474 AC: 72101 AN: 152072 Hom.: 17500 Cov.: 33 AF XY: 0.479 AC XY: 35626 AN XY: 74340

African (AFR) AF: 0.389 AC: 16149 AN: 41470

American (AMR) AF: 0.514 AC: 7853 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1731 AN: 3468

East Asian (EAS) AF: 0.515 AC: 2663 AN: 5172

South Asian (SAS) AF: 0.629 AC: 3030 AN: 4814

European-Finnish (FIN) AF: 0.536 AC: 5661 AN: 10566

Middle Eastern (MID) AF: 0.628 AC: 182 AN: 290

European-Non Finnish (NFE) AF: 0.488 AC: 33200 AN: 67984

Other (OTH) AF: 0.477 AC: 1009 AN: 2114

Alfa AF: 0.471 Hom.: 8815

Bravo AF: 0.468

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2769967; hg19: chr9-81889358;