chr13-105444463-A-G

Variant names:

• chr13-105444463-A-G
• rs11618212

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 0.176 in 152,212 control chromosomes in the GnomAD database, including 2,616 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 0.18 (2616 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.52
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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: 0.176 AC: 26774 AN: 152094 Hom.: 2618 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.176 AC: 26785 AN: 152212 Hom.: 2616 Cov.: 33 AF XY: 0.178 AC XY: 13219 AN XY: 74426

African (AFR) AF: 0.0985 AC: 4094 AN: 41556

American (AMR) AF: 0.148 AC: 2263 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 866 AN: 3472

East Asian (EAS) AF: 0.124 AC: 640 AN: 5168

South Asian (SAS) AF: 0.201 AC: 970 AN: 4828

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10578

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14918 AN: 68002

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.202 Hom.: 10634

Bravo AF: 0.163

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.7
DANN	Benign	0.78
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs11618212; hg19: chr13-106096812;