13-72580085-G-A

Position:

• chr13-72580085-G-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 0.442 in 151,970 control chromosomes in the GnomAD database, including 15,562 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 0.44 (15562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 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: 0.442 AC: 67101 AN: 151850 Hom.: 15550 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.442 AC: 67150 AN: 151970 Hom.: 15562 Cov.: 32 AF XY: 0.443 AC XY: 32872 AN XY: 74240

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.447

Alfa AF: 0.488 Hom.: 24341

Bravo AF: 0.439

Asia WGS AF: 0.419 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1124204; hg19: chr13-73154223;