rs17425287

Variant names:

• chr1-79820726-T-C
• rs17425287

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 0.509 in 151,762 control chromosomes in the GnomAD database, including 20,188 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 (20188 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77185 AN: 151644 Hom.: 20179 Cov.: 30

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.509 AC: 77228 AN: 151762 Hom.: 20188 Cov.: 30 AF XY: 0.513 AC XY: 38029 AN XY: 74146

African (AFR) AF: 0.418 AC: 17287 AN: 41388

American (AMR) AF: 0.596 AC: 9074 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2255 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1585 AN: 5166

South Asian (SAS) AF: 0.530 AC: 2548 AN: 4804

European-Finnish (FIN) AF: 0.606 AC: 6347 AN: 10478

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36445 AN: 67908

Other (OTH) AF: 0.514 AC: 1086 AN: 2112

Alfa AF: 0.539 Hom.: 37174

Bravo AF: 0.502

Asia WGS AF: 0.417 AC: 1447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.50
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs17425287; hg19: chr1-80286411; COSMIC: COSV59960591;