chr5-38249615-C-T

Variant names:

• chr5-38249615-C-T
• rs3901174

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 0.275 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.161 AC: 6650 AN: 41318

American (AMR) AF: 0.287 AC: 4358 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.149 AC: 768 AN: 5158

South Asian (SAS) AF: 0.268 AC: 1271 AN: 4750

European-Finnish (FIN) AF: 0.309 AC: 3233 AN: 10474

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23302 AN: 67824

Other (OTH) AF: 0.289 AC: 609 AN: 2104

Alfa AF: 0.306 Hom.: 11741

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
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs3901174; hg19: chr5-38249717;