rs725656

Variant names:

• chr3-184808420-C-T
• rs725656

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.215 in 152,158 control chromosomes in the GnomAD database, including 4,539 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 0.22 (4539 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.448
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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: 0.215 AC: 32732 AN: 152040 Hom.: 4539 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.215 AC: 32747 AN: 152158 Hom.: 4539 Cov.: 33 AF XY: 0.231 AC XY: 17177 AN XY: 74380

African (AFR) AF: 0.107 AC: 4461 AN: 41532

American (AMR) AF: 0.322 AC: 4922 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 803 AN: 3468

East Asian (EAS) AF: 0.625 AC: 3234 AN: 5178

South Asian (SAS) AF: 0.404 AC: 1947 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3534 AN: 10570

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13166 AN: 67994

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.200 Hom.: 477

Bravo AF: 0.207

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	8.8
DANN	Benign	0.56
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs725656; hg19: chr3-184526208;