5-21186217-T-C

Variant names:

• chr5-21186217-T-C
• rs159171

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 0.0644 in 152,050 control chromosomes in the GnomAD database, including 396 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 0.064 (396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0644 AC: 9781 AN: 151932 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0644 AC: 9786 AN: 152050 Hom.: 396 Cov.: 32 AF XY: 0.0692 AC XY: 5145 AN XY: 74326

African (AFR) AF: 0.102 AC: 4248 AN: 41494

American (AMR) AF: 0.0366 AC: 559 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.0925 AC: 479 AN: 5176

South Asian (SAS) AF: 0.101 AC: 488 AN: 4828

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10580

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0342 AC: 2326 AN: 67914

Other (OTH) AF: 0.0540 AC: 114 AN: 2110

Alfa AF: 0.0448 Hom.: 347

Bravo AF: 0.0592

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.53
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs159171; hg19: chr5-21186326;