rs4856346

Variant names:

• chr3-81453504-T-G
• rs4856346

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 0.661 in 151,836 control chromosomes in the GnomAD database, including 33,535 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 0.66 (33535 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 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: 0.661 AC: 100295 AN: 151718 Hom.: 33520 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.661 AC: 100352 AN: 151836 Hom.: 33535 Cov.: 31 AF XY: 0.657 AC XY: 48733 AN XY: 74196

African (AFR) AF: 0.560 AC: 23180 AN: 41424

American (AMR) AF: 0.685 AC: 10434 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2720 AN: 3462

East Asian (EAS) AF: 0.508 AC: 2599 AN: 5116

South Asian (SAS) AF: 0.711 AC: 3421 AN: 4810

European-Finnish (FIN) AF: 0.627 AC: 6629 AN: 10576

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 48935 AN: 67894

Other (OTH) AF: 0.688 AC: 1452 AN: 2112

Alfa AF: 0.701 Hom.: 90533

Bravo AF: 0.659

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.42
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs4856346; hg19: chr3-81502655;