13-72338200-G-T

Variant names:

• chr13-72338200-G-T
• rs9564897

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 0.262 in 152,000 control chromosomes in the GnomAD database, including 6,204 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 0.26 (6204 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.262 AC: 39779 AN: 151882 Hom.: 6206 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.262 AC: 39769 AN: 152000 Hom.: 6204 Cov.: 32 AF XY: 0.258 AC XY: 19135 AN XY: 74302

African (AFR) AF: 0.108 AC: 4491 AN: 41472

American (AMR) AF: 0.328 AC: 5001 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3470

East Asian (EAS) AF: 0.0408 AC: 211 AN: 5172

South Asian (SAS) AF: 0.162 AC: 779 AN: 4806

European-Finnish (FIN) AF: 0.325 AC: 3422 AN: 10534

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24158 AN: 67958

Other (OTH) AF: 0.264 AC: 558 AN: 2112

Alfa AF: 0.315 Hom.: 4871

Bravo AF: 0.256

Asia WGS AF: 0.0930 AC: 324 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	0.43
DANN	Benign	0.51
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs9564897; hg19: chr13-72912338;