rs351629

chr5-40192924-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 0.305 in 151,902 control chromosomes in the GnomAD database, including 7,294 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 0.30 (7294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.305 AC: 46309 AN: 151784 Hom.: 7292 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.305 AC: 46325 AN: 151902 Hom.: 7294 Cov.: 32 AF XY: 0.304 AC XY: 22585 AN XY: 74208

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.305

Alfa AF: 0.328 Hom.: 1071

Bravo AF: 0.296

Asia WGS AF: 0.244 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.28
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs351629; hg19: chr5-40193026;