13-88023507-A-C

Variant names:

• chr13-88023507-A-C
• rs1413280

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 0.471 in 151,562 control chromosomes in the GnomAD database, including 19,083 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 0.47 (19083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -9.15
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 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: 0.471 AC: 71266 AN: 151444 Hom.: 19057 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.471 AC: 71329 AN: 151562 Hom.: 19083 Cov.: 31 AF XY: 0.469 AC XY: 34717 AN XY: 74062

African (AFR) AF: 0.741 AC: 30684 AN: 41402

American (AMR) AF: 0.365 AC: 5547 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1658 AN: 3458

East Asian (EAS) AF: 0.352 AC: 1805 AN: 5134

South Asian (SAS) AF: 0.527 AC: 2535 AN: 4810

European-Finnish (FIN) AF: 0.339 AC: 3576 AN: 10538

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24171 AN: 67734

Other (OTH) AF: 0.456 AC: 959 AN: 2104

Alfa AF: 0.284 Hom.: 801

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0030
DANN	Benign	0.23
PhyloP100		-9.2

Splicing

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

Other links and lift over

dbSNP: rs1413280; hg19: chr13-88675762;