rs690860

Variant names:

• chr13-34122599-T-C
• rs690860

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 0.414 in 151,840 control chromosomes in the GnomAD database, including 13,453 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 0.41 (13453 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 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: 0.414 AC: 62747 AN: 151720 Hom.: 13451 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.414 AC: 62786 AN: 151840 Hom.: 13453 Cov.: 31 AF XY: 0.411 AC XY: 30535 AN XY: 74218

African (AFR) AF: 0.492 AC: 20359 AN: 41374

American (AMR) AF: 0.331 AC: 5048 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2753 AN: 5138

South Asian (SAS) AF: 0.515 AC: 2471 AN: 4800

European-Finnish (FIN) AF: 0.322 AC: 3398 AN: 10544

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25897 AN: 67958

Other (OTH) AF: 0.388 AC: 818 AN: 2106

Alfa AF: 0.397 Hom.: 37631

Bravo AF: 0.415

Asia WGS AF: 0.486 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.024
DANN	Benign	0.56
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs690860; hg19: chr13-34696736;