rs4445746

Variant names:

• chr13-30767298-G-A
• rs4445746

Your query was ambiguous. Multiple possible variants found:

• chr13-30767298-G-A
• chr13-30767298-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.246 in 151,936 control chromosomes in the GnomAD database, including 4,743 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 0.25 (4743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 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: 0.246 AC: 37343 AN: 151816 Hom.: 4749 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.246 AC: 37346 AN: 151936 Hom.: 4743 Cov.: 32 AF XY: 0.246 AC XY: 18260 AN XY: 74264

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.233

Alfa AF: 0.217 Hom.: 2103

Bravo AF: 0.242

Asia WGS AF: 0.241 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4445746; hg19: chr13-31341435;