chr5-132122104-C-G

Position:

• chr5-132122104-C-G

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 0.291 in 151,732 control chromosomes in the GnomAD database, including 7,884 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 0.29 (7884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44028 AN: 151614 Hom.: 7853 Cov.: 32

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.291 AC: 44119 AN: 151732 Hom.: 7884 Cov.: 32 AF XY: 0.289 AC XY: 21432 AN XY: 74252

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.246

Alfa AF: 0.120 Hom.: 183

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.74
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs555817; hg19: chr5-131457797;