rs1902272

Variant names:

• chr13-31551178-T-C
• rs1902272

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 0.313 in 151,782 control chromosomes in the GnomAD database, including 7,782 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 0.31 (7782 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567

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 (SAS) allele frequency at 95% confidence interval = 0.556 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: 0.313 AC: 47489 AN: 151664 Hom.: 7770 Cov.: 30

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.313 AC: 47526 AN: 151782 Hom.: 7782 Cov.: 30 AF XY: 0.319 AC XY: 23623 AN XY: 74160

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.324

Alfa AF: 0.321 Hom.: 15954

Bravo AF: 0.311

Asia WGS AF: 0.440 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1902272; hg19: chr13-32125315;