rs396045

Variant names:

• chr5-25841504-G-A
• rs396045

Your query was ambiguous. Multiple possible variants found:

• chr5-25841504-G-A
• chr5-25841504-G-C
• chr5-25841504-G-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 0.295 in 151,778 control chromosomes in the GnomAD database, including 7,087 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 (7087 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.295 AC: 44815 AN: 151660 Hom.: 7085 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.295 AC: 44841 AN: 151778 Hom.: 7087 Cov.: 32 AF XY: 0.298 AC XY: 22129 AN XY: 74152

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.314

Alfa AF: 0.349 Hom.: 16058

Bravo AF: 0.285

Asia WGS AF: 0.286 AC: 993 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
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: rs396045; hg19: chr5-25841613;