rs9301112

Variant names:

• chr13-106191668-T-A
• rs9301112

Your query was ambiguous. Multiple possible variants found:

• chr13-106191668-T-A
• chr13-106191668-T-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 0.572 in 152,038 control chromosomes in the GnomAD database, including 27,687 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 0.57 (27687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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: 0.573 AC: 87002 AN: 151922 Hom.: 27686 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.572 AC: 87017 AN: 152038 Hom.: 27687 Cov.: 32 AF XY: 0.574 AC XY: 42678 AN XY: 74316

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.607

Alfa AF: 0.629 Hom.: 3817

Bravo AF: 0.551

Asia WGS AF: 0.557 AC: 1932 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9301112; hg19: chr13-106844017;