rs739856

Positions:

• chr12-47574240-A-G
• chr12-47574240-A-T

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 0.322 in 152,124 control chromosomes in the GnomAD database, including 9,488 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 0.32 (9488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

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 = 0.435 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: 0.322 AC: 49013 AN: 152006 Hom.: 9487 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.322 AC: 49012 AN: 152124 Hom.: 9488 Cov.: 32 AF XY: 0.321 AC XY: 23887 AN XY: 74368

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.332

Alfa AF: 0.396 Hom.: 5755

Bravo AF: 0.301

Asia WGS AF: 0.294 AC: 1022 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739856; hg19: chr12-47968023;