chr9-105666173-C-G

Variant names:

• chr9-105666173-C-G
• rs7867775

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 0.537 in 148,498 control chromosomes in the GnomAD database, including 24,093 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 0.54 (24093 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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: 0.537 AC: 79694 AN: 148398 Hom.: 24050 Cov.: 25

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.537 AC: 79782 AN: 148498 Hom.: 24093 Cov.: 25 AF XY: 0.537 AC XY: 38715 AN XY: 72126

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.551

Alfa AF: 0.452 Hom.: 2158

Bravo AF: 0.561

Asia WGS AF: 0.531 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.0
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7867775; hg19: chr9-108428454;