rs12445135

Positions:

• chr16-27374185-G-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 0.0359 in 152,252 control chromosomes in the GnomAD database, including 216 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 0.036 (216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.1 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: 0.0359 AC: 5465 AN: 152134 Hom.: 215 Cov.: 32

Gnomad AFR AF: 0.00816

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0377

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

GnomAD4 genome AF: 0.0359 AC: 5466 AN: 152252 Hom.: 216 Cov.: 32 AF XY: 0.0393 AC XY: 2925 AN XY: 74456

Gnomad4 AFR AF: 0.00813

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.0734

Gnomad4 FIN AF: 0.0588

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0316 Hom.: 28

Bravo AF: 0.0384

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12445135; hg19: chr16-27385506;