chr5-109611749-C-T

Variant names:

• chr5-109611749-C-T
• rs2201015

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 0.239 in 151,966 control chromosomes in the GnomAD database, including 5,016 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 0.24 (5016 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 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: 0.239 AC: 36296 AN: 151848 Hom.: 5008 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.239 AC: 36329 AN: 151966 Hom.: 5016 Cov.: 31 AF XY: 0.254 AC XY: 18888 AN XY: 74264

African (AFR) AF: 0.200 AC: 8304 AN: 41456

American (AMR) AF: 0.342 AC: 5226 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2813 AN: 5138

South Asian (SAS) AF: 0.292 AC: 1405 AN: 4810

European-Finnish (FIN) AF: 0.366 AC: 3867 AN: 10560

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13067 AN: 67944

Other (OTH) AF: 0.238 AC: 504 AN: 2114

Alfa AF: 0.204 Hom.: 1476

Bravo AF: 0.238

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.098
DANN	Benign	0.61
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2201015; hg19: chr5-108947450; COSMIC: COSV60181845;