rs3824491

Positions:

• chr9-95606595-C-A
• chr9-95606595-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 0.0858 in 152,186 control chromosomes in the GnomAD database, including 616 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 0.086 (616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.102 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: 0.0858 AC: 13049 AN: 152068 Hom.: 615 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.0575

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.0974

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0858 AC: 13058 AN: 152186 Hom.: 616 Cov.: 32 AF XY: 0.0870 AC XY: 6470 AN XY: 74410

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.0575

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0699

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0974

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0745 Hom.: 238

Bravo AF: 0.0822

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.032
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3824491; hg19: chr9-98368877;