chr9-79124770-T-C

Variant names:

• chr9-79124770-T-C
• rs11138082

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 0.199 in 152,098 control chromosomes in the GnomAD database, including 3,139 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 0.20 (3139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 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: 0.199 AC: 30235 AN: 151980 Hom.: 3140 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.199 AC: 30248 AN: 152098 Hom.: 3139 Cov.: 32 AF XY: 0.197 AC XY: 14645 AN XY: 74366

African (AFR) AF: 0.218 AC: 9052 AN: 41470

American (AMR) AF: 0.158 AC: 2413 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 781 AN: 3466

East Asian (EAS) AF: 0.145 AC: 752 AN: 5170

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4822

European-Finnish (FIN) AF: 0.140 AC: 1480 AN: 10596

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13729 AN: 67974

Other (OTH) AF: 0.184 AC: 388 AN: 2112

Alfa AF: 0.208 Hom.: 1824

Bravo AF: 0.200

Asia WGS AF: 0.179 AC: 620 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.62
DANN	Benign	0.56
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs11138082; hg19: chr9-81739686;