rs3901174

chr5-38249615-C-T

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 0.275 in 151,484 control chromosomes in the GnomAD database, including 6,289 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 0.27 (6289 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.991

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.275 AC: 41631 AN: 151362 Hom.: 6295 Cov.: 30

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.275 AC: 41624 AN: 151484 Hom.: 6289 Cov.: 30 AF XY: 0.273 AC XY: 20196 AN XY: 73970

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.289

Alfa AF: 0.299 Hom.: 1718

Bravo AF: 0.270

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	12
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3901174; hg19: chr5-38249717;