13-73355754-A-G

Position:

• chr13-73355754-A-G

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 0.24 in 152,012 control chromosomes in the GnomAD database, including 4,456 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 0.24 (4456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 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: 0.240 AC: 36442 AN: 151894 Hom.: 4449 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.240 AC: 36477 AN: 152012 Hom.: 4456 Cov.: 32 AF XY: 0.242 AC XY: 17986 AN XY: 74298

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.245

Alfa AF: 0.237 Hom.: 6178

Bravo AF: 0.237

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12870000; hg19: chr13-73929891; COSMIC: COSV69363913;