13-111569284-C-T

Variant names:

• chr13-111569284-C-T
• rs1163623

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 152,242 control chromosomes in the GnomAD database, including 55,403 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 (55403 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	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: 129348 AN: 152124 Hom.: 55376 Cov.: 33

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.850 AC: 129429 AN: 152242 Hom.: 55403 Cov.: 33 AF XY: 0.856 AC XY: 63721 AN XY: 74428

African (AFR) AF: 0.749 AC: 31097 AN: 41508

American (AMR) AF: 0.901 AC: 13775 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.880 AC: 3057 AN: 3472

East Asian (EAS) AF: 0.965 AC: 5000 AN: 5184

South Asian (SAS) AF: 0.915 AC: 4414 AN: 4824

European-Finnish (FIN) AF: 0.935 AC: 9923 AN: 10618

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

European-Non Finnish (NFE) AF: 0.871 AC: 59283 AN: 68028

Other (OTH) AF: 0.862 AC: 1820 AN: 2112

Alfa AF: 0.859 Hom.: 76162

Bravo AF: 0.843

Asia WGS AF: 0.918 AC: 3193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.6
DANN	Benign	0.72
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1163623; hg19: chr13-112221631;