rs555212

Variant names:

• chr13-113102226-A-G
• rs555212

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 0.786 in 152,216 control chromosomes in the GnomAD database, including 47,503 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 0.79 (47503 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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: 0.786 AC: 119540 AN: 152098 Hom.: 47463 Cov.: 33

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.786 AC: 119629 AN: 152216 Hom.: 47503 Cov.: 33 AF XY: 0.782 AC XY: 58186 AN XY: 74414

African (AFR) AF: 0.870 AC: 36132 AN: 41544

American (AMR) AF: 0.742 AC: 11347 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3209 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2861 AN: 5188

South Asian (SAS) AF: 0.845 AC: 4083 AN: 4834

European-Finnish (FIN) AF: 0.678 AC: 7168 AN: 10576

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52199 AN: 67990

Other (OTH) AF: 0.807 AC: 1706 AN: 2114

Alfa AF: 0.776 Hom.: 182746

Bravo AF: 0.788

Asia WGS AF: 0.702 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs555212; hg19: chr13-113756540;