rs12596270

Variant names:

• chr16-54810069-A-G
• rs12596270

Your query was ambiguous. Multiple possible variants found:

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

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 0.432 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.327 AC: 13549 AN: 41486

American (AMR) AF: 0.409 AC: 6242 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3470

East Asian (EAS) AF: 0.0365 AC: 189 AN: 5174

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4822

European-Finnish (FIN) AF: 0.570 AC: 6021 AN: 10566

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35450 AN: 67972

Other (OTH) AF: 0.428 AC: 905 AN: 2116

Alfa AF: 0.466 Hom.: 6911

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12596270; hg19: chr16-54843981;