13-22654552-C-A

Position:

• chr13-22654552-C-A

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 0.382 in 151,994 control chromosomes in the GnomAD database, including 12,618 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 0.38 (12618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58005 AN: 151874 Hom.: 12595 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.382 AC: 58076 AN: 151994 Hom.: 12618 Cov.: 32 AF XY: 0.382 AC XY: 28371 AN XY: 74290

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.357

Alfa AF: 0.288 Hom.: 14914

Bravo AF: 0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
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: rs1034200; hg19: chr13-23228691;