rs3802344

chr9-130658892-G-A

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 0.0607 in 152,138 control chromosomes in the GnomAD database, including 327 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 0.061 (327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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: 0.0605 AC: 9204 AN: 152020 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0492

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0607 AC: 9228 AN: 152138 Hom.: 327 Cov.: 32 AF XY: 0.0612 AC XY: 4554 AN XY: 74388

Gnomad4 AFR AF: 0.0489

Gnomad4 AMR AF: 0.0829

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.0213

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0492

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.0649 Hom.: 150

Bravo AF: 0.0607

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.6
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3802344; hg19: chr9-133534279;