rs12920590

Variant names:

• chr16-67386700-T-C
• rs12920590

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 0.26 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
• Publications: 12 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0636 AC: 2643 AN: 41530

American (AMR) AF: 0.244 AC: 3729 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3470

East Asian (EAS) AF: 0.159 AC: 821 AN: 5176

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4830

European-Finnish (FIN) AF: 0.373 AC: 3943 AN: 10584

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24204 AN: 67948

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.326 Hom.: 12874

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
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs12920590; hg19: chr16-67420603;