5-109611586-T-C

Variant names:

• chr5-109611586-T-C
• rs2201016

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 0.22 in 152,088 control chromosomes in the GnomAD database, including 4,434 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 0.22 (4434 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 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: 0.220 AC: 33379 AN: 151970 Hom.: 4429 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.220 AC: 33405 AN: 152088 Hom.: 4434 Cov.: 31 AF XY: 0.235 AC XY: 17475 AN XY: 74334

African (AFR) AF: 0.156 AC: 6485 AN: 41520

American (AMR) AF: 0.334 AC: 5108 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 684 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2886 AN: 5168

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3597 AN: 10542

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.182 AC: 12375 AN: 67980

Other (OTH) AF: 0.227 AC: 480 AN: 2116

Alfa AF: 0.194 Hom.: 1306

Bravo AF: 0.220

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.68
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2201016; hg19: chr5-108947287; COSMIC: COSV60181840;