rs13074501

Positions:

• chr3-146553583-G-A

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 0.429 in 151,812 control chromosomes in the GnomAD database, including 14,484 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 (14484 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65100 AN: 151694 Hom.: 14438 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.429 AC: 65203 AN: 151812 Hom.: 14484 Cov.: 31 AF XY: 0.430 AC XY: 31924 AN XY: 74168

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.392

Alfa AF: 0.415 Hom.: 2020

Bravo AF: 0.425

Asia WGS AF: 0.306 AC: 1066 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	2.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13074501; hg19: chr3-146271370;