rs1903937

Variant names:

• chr12-45127704-C-T
• rs1903937

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 0.292 in 151,688 control chromosomes in the GnomAD database, including 7,443 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 0.29 (7443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.239

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.514 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: 0.292 AC: 44252 AN: 151570 Hom.: 7446 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.292 AC: 44254 AN: 151688 Hom.: 7443 Cov.: 31 AF XY: 0.299 AC XY: 22164 AN XY: 74110

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.318

Alfa AF: 0.309 Hom.: 1017

Bravo AF: 0.267

Asia WGS AF: 0.374 AC: 1301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1903937; hg19: chr12-45521487;