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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.179 AC: 7411 AN: 41370

American (AMR) AF: 0.287 AC: 4378 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1310 AN: 5140

South Asian (SAS) AF: 0.343 AC: 1653 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3613 AN: 10474

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23913 AN: 67928

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.336 Hom.: 24060

Bravo AF: 0.285

Asia WGS AF: 0.286 AC: 993 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.41
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs396045; hg19: chr5-25841613;