9-117679668-C-T

Variant names:

• chr9-117679668-C-T
• rs1329057

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 0.755 in 151,200 control chromosomes in the GnomAD database, including 43,468 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 (43468 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 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: 0.755 AC: 114027 AN: 151082 Hom.: 43453 Cov.: 31

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.755 AC: 114097 AN: 151200 Hom.: 43468 Cov.: 31 AF XY: 0.752 AC XY: 55552 AN XY: 73870

African (AFR) AF: 0.647 AC: 26747 AN: 41364

American (AMR) AF: 0.807 AC: 12228 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2655 AN: 3448

East Asian (EAS) AF: 0.749 AC: 3844 AN: 5132

South Asian (SAS) AF: 0.824 AC: 3969 AN: 4818

European-Finnish (FIN) AF: 0.694 AC: 7319 AN: 10546

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 54698 AN: 67420

Other (OTH) AF: 0.771 AC: 1624 AN: 2106

Alfa AF: 0.798 Hom.: 79752

Bravo AF: 0.757

Asia WGS AF: 0.789 AC: 2743 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs1329057; hg19: chr9-120441946;