rs9849690

Positions:

• chr3-184610232-G-A
• chr3-184610232-G-C

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 0.465 in 151,782 control chromosomes in the GnomAD database, including 16,827 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 0.47 (16827 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70553 AN: 151664 Hom.: 16810 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.465 AC: 70607 AN: 151782 Hom.: 16827 Cov.: 30 AF XY: 0.468 AC XY: 34708 AN XY: 74190

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.479

Alfa AF: 0.472 Hom.: 22884

Bravo AF: 0.457

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9849690; hg19: chr3-184328020;