rs3758317

Variant names:

• chr9-84667700-C-T
• rs3758317

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0529 AC: 2197 AN: 41550

American (AMR) AF: 0.0947 AC: 1449 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.0631 AC: 327 AN: 5180

South Asian (SAS) AF: 0.136 AC: 653 AN: 4814

European-Finnish (FIN) AF: 0.153 AC: 1622 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11448 AN: 67998

Other (OTH) AF: 0.144 AC: 304 AN: 2108

Alfa AF: 0.157 Hom.: 3321

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs3758317; hg19: chr9-87282615;