rs12350739

Variant names:

• chr9-16885019-G-A
• rs12350739

Your query was ambiguous. Multiple possible variants found:

• chr9-16885019-G-A
• chr9-16885019-G-C
• chr9-16885019-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.387 in 150,700 control chromosomes in the GnomAD database, including 15,349 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 0.39 (15349 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 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: 0.387 AC: 58351 AN: 150586 Hom.: 15349 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.00310

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.387 AC: 58346 AN: 150700 Hom.: 15349 Cov.: 31 AF XY: 0.379 AC XY: 27949 AN XY: 73652

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.00311

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.392

Alfa AF: 0.506 Hom.: 4974

Bravo AF: 0.361

Asia WGS AF: 0.0720 AC: 251 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12350739; hg19: chr9-16885017;