13-30169232-T-C

Position:

• chr13-30169232-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 0.624 in 152,046 control chromosomes in the GnomAD database, including 29,744 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 0.62 (29744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94772 AN: 151928 Hom.: 29711 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.624 AC: 94849 AN: 152046 Hom.: 29744 Cov.: 32 AF XY: 0.625 AC XY: 46452 AN XY: 74330

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.609

Alfa AF: 0.620 Hom.: 3601

Bravo AF: 0.626

Asia WGS AF: 0.568 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073230; hg19: chr13-30743369;