rs12346562

Variant names:

• chr9-11018077-C-A
• rs12346562

Your query was ambiguous. Multiple possible variants found:

• chr9-11018077-C-A
• chr9-11018077-C-G
• chr9-11018077-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 0.24 in 151,684 control chromosomes in the GnomAD database, including 4,660 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 0.24 (4660 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.277 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: 0.240 AC: 36344 AN: 151568 Hom.: 4662 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.240 AC: 36362 AN: 151684 Hom.: 4660 Cov.: 33 AF XY: 0.238 AC XY: 17660 AN XY: 74120

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0481

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.271

Alfa AF: 0.268 Hom.: 8732

Bravo AF: 0.224

Asia WGS AF: 0.150 AC: 522 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12346562; hg19: chr9-11018077;