chr9-17895107-T-C

Position:

• chr9-17895107-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.112 in 152,232 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1090 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17080 AN: 152114 Hom.: 1091 Cov.: 33

Gnomad AFR AF: 0.0593

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.112 AC: 17082 AN: 152232 Hom.: 1090 Cov.: 33 AF XY: 0.110 AC XY: 8151 AN XY: 74438

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.0972

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.130

Alfa AF: 0.139 Hom.: 2275

Bravo AF: 0.110

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10810865; hg19: chr9-17895105;