13-105346321-A-G

Variant names:

• chr13-105346321-A-G
• rs746187

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 0.293 in 152,042 control chromosomes in the GnomAD database, including 7,464 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 0.29 (7464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.381 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: 0.293 AC: 44468 AN: 151926 Hom.: 7466 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.293 AC: 44473 AN: 152042 Hom.: 7464 Cov.: 32 AF XY: 0.289 AC XY: 21507 AN XY: 74314

African (AFR) AF: 0.153 AC: 6340 AN: 41504

American (AMR) AF: 0.228 AC: 3470 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3466

East Asian (EAS) AF: 0.0877 AC: 453 AN: 5166

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4820

European-Finnish (FIN) AF: 0.410 AC: 4332 AN: 10568

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.385 AC: 26178 AN: 67956

Other (OTH) AF: 0.291 AC: 613 AN: 2108

Alfa AF: 0.342 Hom.: 16184

Bravo AF: 0.270

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.34
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs746187; hg19: chr13-105998672;