chr13-90012528-G-A

Variant names:

• chr13-90012528-G-A
• rs2805657

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 0.0463 in 152,052 control chromosomes in the GnomAD database, including 237 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 0.046 (237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815
• Publications: 0 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 (AFR) allele frequency at 95% confidence interval = 0.0787 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: 0.0462 AC: 7022 AN: 151934 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.00676

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0239

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0321

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0463 AC: 7036 AN: 152052 Hom.: 237 Cov.: 32 AF XY: 0.0463 AC XY: 3443 AN XY: 74320

African (AFR) AF: 0.0810 AC: 3361 AN: 41500

American (AMR) AF: 0.0367 AC: 560 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.00658 AC: 34 AN: 5166

South Asian (SAS) AF: 0.0591 AC: 284 AN: 4808

European-Finnish (FIN) AF: 0.0239 AC: 253 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0321 AC: 2181 AN: 67938

Other (OTH) AF: 0.0497 AC: 105 AN: 2114

Alfa AF: 0.0370 Hom.: 53

Bravo AF: 0.0480

Asia WGS AF: 0.0330 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.74
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2805657; hg19: chr13-90664782;