rs2188468

chr5-136663359-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;