rs9512699

Variant names:

• chr13-27455759-G-A
• rs9512699

Your query was ambiguous. Multiple possible variants found:

• chr13-27455759-G-A
• chr13-27455759-G-C

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 0.823 in 152,082 control chromosomes in the GnomAD database, including 51,733 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 0.82 (51733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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: 0.823 AC: 125116 AN: 151964 Hom.: 51686 Cov.: 31

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.823 AC: 125219 AN: 152082 Hom.: 51733 Cov.: 31 AF XY: 0.821 AC XY: 60994 AN XY: 74328

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.800

Gnomad4 OTH AF: 0.810

Alfa AF: 0.804 Hom.: 42484

Bravo AF: 0.835

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9512699; hg19: chr13-28029896;