chr13-72075234-G-A

Position:

• chr13-72075234-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 0.7 in 151,846 control chromosomes in the GnomAD database, including 38,303 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 (38303 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 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: 0.700 AC: 106184 AN: 151728 Hom.: 38291 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.718

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

GnomAD4 genome AF: 0.700 AC: 106236 AN: 151846 Hom.: 38303 Cov.: 31 AF XY: 0.699 AC XY: 51857 AN XY: 74184

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.717

Alfa AF: 0.700 Hom.: 5526

Bravo AF: 0.693

Asia WGS AF: 0.730 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	12
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2325443; hg19: chr13-72649372;