13-64362111-G-A

Variant names:

• chr13-64362111-G-A
• rs9571178

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 0.429 in 151,612 control chromosomes in the GnomAD database, including 14,399 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 0.43 (14399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.514 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: 0.429 AC: 65011 AN: 151494 Hom.: 14376 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.429 AC: 65088 AN: 151612 Hom.: 14399 Cov.: 31 AF XY: 0.425 AC XY: 31441 AN XY: 74062

African (AFR) AF: 0.412 AC: 17021 AN: 41276

American (AMR) AF: 0.523 AC: 7959 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1423 AN: 3466

East Asian (EAS) AF: 0.237 AC: 1216 AN: 5132

South Asian (SAS) AF: 0.377 AC: 1815 AN: 4812

European-Finnish (FIN) AF: 0.308 AC: 3230 AN: 10500

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30911 AN: 67896

Other (OTH) AF: 0.435 AC: 918 AN: 2112

Alfa AF: 0.447 Hom.: 69674

Bravo AF: 0.445

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.1
DANN	Benign	0.95
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs9571178; hg19: chr13-64936243;