rs1902272

Variant names:

• chr13-31551178-T-C
• rs1902272

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 0.313 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.269 AC: 11118 AN: 41382

American (AMR) AF: 0.341 AC: 5200 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3462

East Asian (EAS) AF: 0.370 AC: 1904 AN: 5142

South Asian (SAS) AF: 0.573 AC: 2749 AN: 4794

European-Finnish (FIN) AF: 0.315 AC: 3317 AN: 10520

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20860 AN: 67904

Other (OTH) AF: 0.324 AC: 685 AN: 2112

Alfa AF: 0.316 Hom.: 32093

Bravo AF: 0.311

Asia WGS AF: 0.440 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.86
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1902272; hg19: chr13-32125315;