rs12596270

Positions:

• chr16-54810069-A-G
• chr16-54810069-A-T

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 0.432 in 152,090 control chromosomes in the GnomAD database, including 15,482 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 (15482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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: 0.432 AC: 65670 AN: 151972 Hom.: 15481 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.432 AC: 65681 AN: 152090 Hom.: 15482 Cov.: 32 AF XY: 0.428 AC XY: 31795 AN XY: 74350

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.0365

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.428

Alfa AF: 0.466 Hom.: 5512

Bravo AF: 0.417

Asia WGS AF: 0.141 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12596270; hg19: chr16-54843981;