rs351629

Variant names:

• chr5-40192924-G-C
• rs351629

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.272 AC: 11267 AN: 41438

American (AMR) AF: 0.268 AC: 4095 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3466

East Asian (EAS) AF: 0.192 AC: 990 AN: 5162

South Asian (SAS) AF: 0.231 AC: 1113 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3932 AN: 10534

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23104 AN: 67904

Other (OTH) AF: 0.305 AC: 642 AN: 2104

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs351629; hg19: chr5-40193026;