rs905648

Variant names:

• chr3-15523815-C-T
• rs905648

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 0.416 in 152,044 control chromosomes in the GnomAD database, including 14,316 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 0.42 (14316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.605 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: 0.415 AC: 63096 AN: 151926 Hom.: 14274 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.416 AC: 63207 AN: 152044 Hom.: 14316 Cov.: 32 AF XY: 0.415 AC XY: 30834 AN XY: 74338

African (AFR) AF: 0.577 AC: 23928 AN: 41434

American (AMR) AF: 0.448 AC: 6855 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1115 AN: 3468

East Asian (EAS) AF: 0.623 AC: 3215 AN: 5164

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4816

European-Finnish (FIN) AF: 0.250 AC: 2648 AN: 10576

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22323 AN: 67984

Other (OTH) AF: 0.411 AC: 868 AN: 2110

Alfa AF: 0.376 Hom.: 2454

Bravo AF: 0.439

Asia WGS AF: 0.489 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.60
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs905648; hg19: chr3-15565322;