rs3864785

Variant names:

• chr9-7603506-G-C
• rs3864785

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 0.897 in 152,186 control chromosomes in the GnomAD database, including 61,274 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 0.90 (61274 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.897 AC: 136402 AN: 152068 Hom.: 61219 Cov.: 33

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.897 AC: 136516 AN: 152186 Hom.: 61274 Cov.: 33 AF XY: 0.900 AC XY: 66947 AN XY: 74400

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.858

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.971

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.884

Alfa AF: 0.892 Hom.: 7512

Bravo AF: 0.896

Asia WGS AF: 0.975 AC: 3391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.026
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3864785; hg19: chr9-7603506;