rs4856162

Variant names:

• chr3-103573382-G-A
• rs4856162

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 0.423 in 151,742 control chromosomes in the GnomAD database, including 15,225 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 (15225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64114 AN: 151622 Hom.: 15172 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.423 AC: 64237 AN: 151742 Hom.: 15225 Cov.: 32 AF XY: 0.431 AC XY: 31970 AN XY: 74182

African (AFR) AF: 0.637 AC: 26400 AN: 41414

American (AMR) AF: 0.445 AC: 6773 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3468

East Asian (EAS) AF: 0.493 AC: 2546 AN: 5166

South Asian (SAS) AF: 0.478 AC: 2306 AN: 4822

European-Finnish (FIN) AF: 0.375 AC: 3958 AN: 10542

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19777 AN: 67822

Other (OTH) AF: 0.434 AC: 913 AN: 2102

Alfa AF: 0.354 Hom.: 19198

Bravo AF: 0.438

Asia WGS AF: 0.543 AC: 1887 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.49
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4856162; hg19: chr3-103292226;