chr11-13170897-G-T

Variant names:

• chr11-13170897-G-T
• rs1481872

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 0.387 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 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: 0.387 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

African (AFR) AF: 0.185 AC: 7671 AN: 41488

American (AMR) AF: 0.424 AC: 6474 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5172

South Asian (SAS) AF: 0.311 AC: 1502 AN: 4826

European-Finnish (FIN) AF: 0.489 AC: 5171 AN: 10572

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33668 AN: 67958

Other (OTH) AF: 0.426 AC: 902 AN: 2116

Alfa AF: 0.413 Hom.: 11431

Bravo AF: 0.377

Asia WGS AF: 0.278 AC: 968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
DANN	Benign	0.70
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1481872; hg19: chr11-13192444;