12-55607543-C-T

Variant names:

• chr12-55607543-C-T
• rs10747758

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 0.495 in 151,954 control chromosomes in the GnomAD database, including 20,841 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 0.50 (20841 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 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: 0.495 AC: 75161 AN: 151836 Hom.: 20788 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.495 AC: 75268 AN: 151954 Hom.: 20841 Cov.: 31 AF XY: 0.498 AC XY: 36966 AN XY: 74266

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.467

Alfa AF: 0.375 Hom.: 4636

Bravo AF: 0.508

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10747758; hg19: chr12-56001327;