chr13-75052353-A-G

Variant names:

• chr13-75052353-A-G
• rs1340902

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 0.514 in 151,912 control chromosomes in the GnomAD database, including 20,975 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 0.51 (20975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 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: 0.514 AC: 78072 AN: 151794 Hom.: 20963 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.514 AC: 78117 AN: 151912 Hom.: 20975 Cov.: 32 AF XY: 0.514 AC XY: 38155 AN XY: 74214

African (AFR) AF: 0.353 AC: 14620 AN: 41458

American (AMR) AF: 0.559 AC: 8501 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2023 AN: 3466

East Asian (EAS) AF: 0.559 AC: 2876 AN: 5146

South Asian (SAS) AF: 0.438 AC: 2108 AN: 4814

European-Finnish (FIN) AF: 0.596 AC: 6291 AN: 10554

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39822 AN: 67940

Other (OTH) AF: 0.534 AC: 1126 AN: 2110

Alfa AF: 0.546 Hom.: 10619

Bravo AF: 0.508

Asia WGS AF: 0.528 AC: 1834 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1340902; hg19: chr13-75626490;