13-46826872-T-C

Variant names:

• chr13-46826872-T-C
• rs9567732

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 0.697 in 152,032 control chromosomes in the GnomAD database, including 38,609 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 0.70 (38609 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.697 AC: 105944 AN: 151914 Hom.: 38581 Cov.: 32

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.697 AC: 106025 AN: 152032 Hom.: 38609 Cov.: 32 AF XY: 0.692 AC XY: 51398 AN XY: 74298

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.703

Alfa AF: 0.629 Hom.: 27706

Bravo AF: 0.726

Asia WGS AF: 0.659 AC: 2295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
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: rs9567732; hg19: chr13-47401007;