rs2188468

Variant names:

• chr5-136663359-G-A
• rs2188468

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0544 in 152,026 control chromosomes in the GnomAD database, including 505 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 0.054 (505 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.608

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0543 AC: 8251 AN: 151908 Hom.: 504 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0262

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.00910

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0544 AC: 8269 AN: 152026 Hom.: 505 Cov.: 33 AF XY: 0.0557 AC XY: 4138 AN XY: 74314

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.00910

Gnomad4 NFE AF: 0.0117

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0338 Hom.: 40

Bravo AF: 0.0588

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2188468; hg19: chr5-135999048;