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
• Publications: 4 publications found

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.501 AC: 20768 AN: 41434

American (AMR) AF: 0.115 AC: 1751 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.0207 AC: 107 AN: 5166

South Asian (SAS) AF: 0.224 AC: 1076 AN: 4806

European-Finnish (FIN) AF: 0.0451 AC: 478 AN: 10596

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.0831 AC: 5651 AN: 68004

Other (OTH) AF: 0.187 AC: 393 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		0.15

Splicing

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

Other links and lift over

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