rs739857

chr12-47574503-A-Cchr12-47574503-A-Gchr12-47574503-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 0.321 in 152,136 control chromosomes in the GnomAD database, including 9,490 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 (9490 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• 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	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48883 AN: 152018 Hom.: 9489 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.321 AC: 48880 AN: 152136 Hom.: 9490 Cov.: 32 AF XY: 0.320 AC XY: 23839 AN XY: 74388

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.331

Alfa AF: 0.413 Hom.: 19950

Bravo AF: 0.299

Asia WGS AF: 0.294 AC: 1023 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.41
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739857; hg19: chr12-47968286;