rs903570

chr12-48874736-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 0.202 in 152,056 control chromosomes in the GnomAD database, including 5,833 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 0.20 (5833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 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: 0.202 AC: 30664 AN: 151938 Hom.: 5809 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0209

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0451

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0831

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.202 AC: 30726 AN: 152056 Hom.: 5833 Cov.: 31 AF XY: 0.198 AC XY: 14747 AN XY: 74348

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0207

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.0451

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.187

Alfa AF: 0.118 Hom.: 727

Bravo AF: 0.216

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs903570; hg19: chr12-49268519; COSMIC: COSV56451767;