rs946808

Positions:

• chr9-79504995-C-A
• chr9-79504995-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 0.244 in 151,890 control chromosomes in the GnomAD database, including 8,280 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 0.24 (8280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.243 AC: 36885 AN: 151772 Hom.: 8229 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.244 AC: 36989 AN: 151890 Hom.: 8280 Cov.: 32 AF XY: 0.234 AC XY: 17340 AN XY: 74244

Gnomad4 AFR AF: 0.594

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0229

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.197

Alfa AF: 0.134 Hom.: 1306

Bravo AF: 0.266

Asia WGS AF: 0.123 AC: 432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	17
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: rs946808; hg19: chr9-82119910;