rs12926540

Variant names:

• chr16-81225382-T-C
• rs12926540

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 0.476 in 151,876 control chromosomes in the GnomAD database, including 18,077 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 0.48 (18077 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.476 AC: 72273 AN: 151756 Hom.: 18075 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.476 AC: 72305 AN: 151876 Hom.: 18077 Cov.: 31 AF XY: 0.482 AC XY: 35809 AN XY: 74220

African (AFR) AF: 0.342 AC: 14157 AN: 41384

American (AMR) AF: 0.507 AC: 7727 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3466

East Asian (EAS) AF: 0.827 AC: 4259 AN: 5152

South Asian (SAS) AF: 0.506 AC: 2438 AN: 4820

European-Finnish (FIN) AF: 0.600 AC: 6336 AN: 10552

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34375 AN: 67960

Other (OTH) AF: 0.454 AC: 958 AN: 2110

Alfa AF: 0.467 Hom.: 2433

Bravo AF: 0.467

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.87
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12926540; hg19: chr16-81258987;