rs1481872

chr11-13170897-G-T

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 0.387 in 152,084 control chromosomes in the GnomAD database, including 12,903 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 0.39 (12903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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 (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58838 AN: 151966 Hom.: 12902 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.387 AC: 58851 AN: 152084 Hom.: 12903 Cov.: 33 AF XY: 0.385 AC XY: 28657 AN XY: 74368

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.426

Alfa AF: 0.454 Hom.: 8189

Bravo AF: 0.377

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.5
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1481872; hg19: chr11-13192444;