13-72142594-G-A

Variant names:

• chr13-72142594-G-A
• rs1326684

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 0.167 in 152,080 control chromosomes in the GnomAD database, including 2,891 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 0.17 (2891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25390 AN: 151962 Hom.: 2880 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.167 AC: 25411 AN: 152080 Hom.: 2891 Cov.: 32 AF XY: 0.175 AC XY: 13014 AN XY: 74342

African (AFR) AF: 0.137 AC: 5674 AN: 41490

American (AMR) AF: 0.282 AC: 4302 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2976 AN: 5126

South Asian (SAS) AF: 0.255 AC: 1234 AN: 4830

European-Finnish (FIN) AF: 0.168 AC: 1778 AN: 10596

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8586 AN: 67982

Other (OTH) AF: 0.173 AC: 365 AN: 2112

Alfa AF: 0.145 Hom.: 3178

Bravo AF: 0.179

Asia WGS AF: 0.351 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs1326684; hg19: chr13-72716732;