rs2009501

Variant names:

• chr5-10159429-T-C
• rs2009501

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 0.291 in 152,092 control chromosomes in the GnomAD database, including 6,945 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 0.29 (6945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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: 0.291 AC: 44297 AN: 151974 Hom.: 6937 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.291 AC: 44308 AN: 152092 Hom.: 6945 Cov.: 32 AF XY: 0.293 AC XY: 21808 AN XY: 74350

African (AFR) AF: 0.205 AC: 8488 AN: 41504

American (AMR) AF: 0.302 AC: 4617 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2674 AN: 5162

South Asian (SAS) AF: 0.340 AC: 1639 AN: 4814

European-Finnish (FIN) AF: 0.290 AC: 3063 AN: 10570

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21334 AN: 67958

Other (OTH) AF: 0.323 AC: 683 AN: 2112

Alfa AF: 0.305 Hom.: 931

Bravo AF: 0.292

Asia WGS AF: 0.426 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.20
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2009501; hg19: chr5-10159541;