9-16911668-C-T

Position:

• chr9-16911668-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.138 in 152,082 control chromosomes in the GnomAD database, including 1,816 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 0.14 (1816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20935 AN: 151964 Hom.: 1815 Cov.: 32

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.138 AC: 20941 AN: 152082 Hom.: 1816 Cov.: 32 AF XY: 0.134 AC XY: 9951 AN XY: 74354

Gnomad4 AFR AF: 0.0458

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0621

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.133

Alfa AF: 0.186 Hom.: 5605

Bravo AF: 0.128

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10810666; hg19: chr9-16911666; COSMIC: COSV60335683;