rs7489413

Variant names:

• chr13-108126028-T-C
• rs7489413

Your query was ambiguous. Multiple possible variants found:

• chr13-108126028-T-C
• chr13-108126028-T-G

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 0.757 in 151,862 control chromosomes in the GnomAD database, including 45,549 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 0.76 (45549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.758 AC: 114976 AN: 151742 Hom.: 45540 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.757 AC: 115014 AN: 151862 Hom.: 45549 Cov.: 32 AF XY: 0.760 AC XY: 56449 AN XY: 74248

African (AFR) AF: 0.505 AC: 20882 AN: 41350

American (AMR) AF: 0.756 AC: 11540 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3090 AN: 3466

East Asian (EAS) AF: 0.731 AC: 3757 AN: 5138

South Asian (SAS) AF: 0.760 AC: 3658 AN: 4814

European-Finnish (FIN) AF: 0.941 AC: 9964 AN: 10590

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.875 AC: 59441 AN: 67914

Other (OTH) AF: 0.776 AC: 1640 AN: 2114

Alfa AF: 0.808 Hom.: 20954

Bravo AF: 0.733

Asia WGS AF: 0.727 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.24
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs7489413; hg19: chr13-108778376;