chr13-111567085-A-G

Variant names:

• chr13-111567085-A-G
• rs1361542

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 0.85 in 152,206 control chromosomes in the GnomAD database, including 55,386 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 0.85 (55386 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 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: 0.850 AC: 129344 AN: 152088 Hom.: 55352 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.878

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.850 AC: 129435 AN: 152206 Hom.: 55386 Cov.: 33 AF XY: 0.856 AC XY: 63743 AN XY: 74424

African (AFR) AF: 0.755 AC: 31309 AN: 41486

American (AMR) AF: 0.899 AC: 13755 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3054 AN: 3470

East Asian (EAS) AF: 0.964 AC: 4987 AN: 5172

South Asian (SAS) AF: 0.914 AC: 4408 AN: 4824

European-Finnish (FIN) AF: 0.933 AC: 9899 AN: 10612

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59152 AN: 68020

Other (OTH) AF: 0.860 AC: 1815 AN: 2110

Alfa AF: 0.857 Hom.: 77283

Bravo AF: 0.843

Asia WGS AF: 0.921 AC: 3203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.21
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs1361542; hg19: chr13-112219432;