rs12453270

chr17-49958675-T-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 0.443 in 151,784 control chromosomes in the GnomAD database, including 18,158 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 0.44 (18158 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67193 AN: 151666 Hom.: 18151 Cov.: 29

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.443 AC: 67205 AN: 151784 Hom.: 18158 Cov.: 29 AF XY: 0.444 AC XY: 32934 AN XY: 74148

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.487

Alfa AF: 0.488 Hom.: 2475

Bravo AF: 0.431

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.6
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12453270; hg19: chr17-48036039;