rs12920590

Positions:

• chr16-67386700-T-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 0.26 in 152,136 control chromosomes in the GnomAD database, including 6,526 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 0.26 (6526 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.261 AC: 39622 AN: 152018 Hom.: 6525 Cov.: 32

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.260 AC: 39620 AN: 152136 Hom.: 6526 Cov.: 32 AF XY: 0.262 AC XY: 19462 AN XY: 74374

Gnomad4 AFR AF: 0.0636

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.281

Alfa AF: 0.344 Hom.: 9581

Bravo AF: 0.242

Asia WGS AF: 0.262 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12920590; hg19: chr16-67420603;