rs3758317

Positions:

• chr9-84667700-C-T

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 0.123 in 152,210 control chromosomes in the GnomAD database, including 1,423 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 0.12 (1423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 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: 0.123 AC: 18717 AN: 152092 Hom.: 1425 Cov.: 32

Gnomad AFR AF: 0.0527

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.0948

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.123 AC: 18719 AN: 152210 Hom.: 1423 Cov.: 32 AF XY: 0.121 AC XY: 9032 AN XY: 74412

Gnomad4 AFR AF: 0.0529

Gnomad4 AMR AF: 0.0947

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0631

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.144

Alfa AF: 0.162 Hom.: 2725

Bravo AF: 0.116

Asia WGS AF: 0.113 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	6.6
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3758317; hg19: chr9-87282615;