rs903570

Variant names:

• chr12-48874736-G-A
• rs903570

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 0.202 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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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 AC: 0.501231 AN: 0.501231

Gnomad4 AMR AF: 0.115 AC: 0.114699 AN: 0.114699

Gnomad4 ASJ AF: 0.115 AC: 0.115495 AN: 0.115495

Gnomad4 EAS AF: 0.0207 AC: 0.0207123 AN: 0.0207123

Gnomad4 SAS AF: 0.224 AC: 0.223887 AN: 0.223887

Gnomad4 FIN AF: 0.0451 AC: 0.0451114 AN: 0.0451114

Gnomad4 NFE AF: 0.0831 AC: 0.0830981 AN: 0.0830981

Gnomad4 OTH AF: 0.187 AC: 0.18661 AN: 0.18661

Alfa AF: 0.107 Hom.: 897

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;