9-117676199-T-C

Variant names:

• chr9-117676199-T-C
• rs1329060

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 0.75 in 151,708 control chromosomes in the GnomAD database, including 44,450 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 0.75 (44450 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 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: 0.750 AC: 113688 AN: 151588 Hom.: 44428 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.750 AC: 113758 AN: 151708 Hom.: 44450 Cov.: 31 AF XY: 0.748 AC XY: 55487 AN XY: 74168

African (AFR) AF: 0.514 AC: 21257 AN: 41344

American (AMR) AF: 0.845 AC: 12837 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2893 AN: 3458

East Asian (EAS) AF: 0.759 AC: 3889 AN: 5126

South Asian (SAS) AF: 0.872 AC: 4198 AN: 4814

European-Finnish (FIN) AF: 0.719 AC: 7613 AN: 10584

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58372 AN: 67866

Other (OTH) AF: 0.785 AC: 1656 AN: 2110

Alfa AF: 0.782 Hom.: 6123

Bravo AF: 0.747

Asia WGS AF: 0.813 AC: 2829 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1329060; hg19: chr9-120438477;