chr13-70236091-G-A

Variant names:

• chr13-70236091-G-A
• rs1928007

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 0.839 in 151,922 control chromosomes in the GnomAD database, including 54,250 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 0.84 (54250 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 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: 0.839 AC: 127323 AN: 151806 Hom.: 54203 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.839 AC: 127424 AN: 151922 Hom.: 54250 Cov.: 33 AF XY: 0.841 AC XY: 62440 AN XY: 74240

African (AFR) AF: 0.673 AC: 27841 AN: 41376

American (AMR) AF: 0.880 AC: 13414 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2913 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4934 AN: 5166

South Asian (SAS) AF: 0.879 AC: 4246 AN: 4830

European-Finnish (FIN) AF: 0.932 AC: 9871 AN: 10588

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.903 AC: 61377 AN: 67940

Other (OTH) AF: 0.839 AC: 1773 AN: 2114

Alfa AF: 0.862 Hom.: 8132

Bravo AF: 0.827

Asia WGS AF: 0.910 AC: 3122 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.30
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs1928007; hg19: chr13-70810223;