chr13-72075234-G-A

Variant names:

• chr13-72075234-G-A
• rs2325443

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.508 AC: 21010 AN: 41356

American (AMR) AF: 0.767 AC: 11693 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2838 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4182 AN: 5154

South Asian (SAS) AF: 0.733 AC: 3534 AN: 4824

European-Finnish (FIN) AF: 0.750 AC: 7913 AN: 10550

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52470 AN: 67936

Other (OTH) AF: 0.717 AC: 1511 AN: 2106

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2325443; hg19: chr13-72649372;