chr13-68956532-G-A

Variant names:

• chr13-68956532-G-A
• rs2066219

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 0.726 in 152,026 control chromosomes in the GnomAD database, including 40,331 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 0.73 (40331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 18 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 (AMR) allele frequency at 95% confidence interval = 0.796 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: 0.725 AC: 110203 AN: 151908 Hom.: 40275 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.726 AC: 110318 AN: 152026 Hom.: 40331 Cov.: 32 AF XY: 0.723 AC XY: 53723 AN XY: 74316

African (AFR) AF: 0.642 AC: 26624 AN: 41440

American (AMR) AF: 0.808 AC: 12331 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2806 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3823 AN: 5170

South Asian (SAS) AF: 0.704 AC: 3392 AN: 4820

European-Finnish (FIN) AF: 0.695 AC: 7344 AN: 10564

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51396 AN: 67974

Other (OTH) AF: 0.734 AC: 1550 AN: 2112

Alfa AF: 0.744 Hom.: 143278

Bravo AF: 0.733

Asia WGS AF: 0.684 AC: 2374 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.24
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs2066219; hg19: chr13-69530664;