5-52660690-G-C

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 0.187 in 152,066 control chromosomes in the GnomAD database, including 2,957 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 0.19 (2957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.187 AC: 28424 AN: 151948 Hom.: 2952 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.00502

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.187 AC: 28456 AN: 152066 Hom.: 2957 Cov.: 32 AF XY: 0.183 AC XY: 13569 AN XY: 74312

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.00503

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.189

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.195

Alfa AF: 0.0991 Hom.: 155

Bravo AF: 0.182

Asia WGS AF: 0.0870 AC: 303 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.22
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2406195; hg19: chr5-51956524;