13-81906466-A-G

Variant names:

• chr13-81906466-A-G
• rs4456389

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 0.387 in 151,922 control chromosomes in the GnomAD database, including 12,069 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 0.39 (12069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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: 0.387 AC: 58774 AN: 151806 Hom.: 12059 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.387 AC: 58825 AN: 151922 Hom.: 12069 Cov.: 32 AF XY: 0.386 AC XY: 28647 AN XY: 74262

African (AFR) AF: 0.524 AC: 21709 AN: 41440

American (AMR) AF: 0.343 AC: 5234 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3466

East Asian (EAS) AF: 0.112 AC: 577 AN: 5174

South Asian (SAS) AF: 0.301 AC: 1450 AN: 4814

European-Finnish (FIN) AF: 0.364 AC: 3850 AN: 10564

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23427 AN: 67904

Other (OTH) AF: 0.346 AC: 730 AN: 2112

Alfa AF: 0.327 Hom.: 3056

Bravo AF: 0.388

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.31
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4456389; hg19: chr13-82480601;