rs4860308

Variant names:

• chr4-68623954-A-T
• rs4860308

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.94 (56846 hom., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.983 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: 0.943 AC: 117288 AN: 124342 Hom.: 56823 Cov.: 20

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.989

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.943 AC: 117338 AN: 124402 Hom.: 56846 Cov.: 20 AF XY: 0.942 AC XY: 55888 AN XY: 59308

African (AFR) AF: 0.844 AC: 30707 AN: 36400

American (AMR) AF: 0.974 AC: 11739 AN: 12050

Ashkenazi Jewish (ASJ) AF: 0.999 AC: 2981 AN: 2984

East Asian (EAS) AF: 1.00 AC: 1288 AN: 1288

South Asian (SAS) AF: 0.997 AC: 2780 AN: 2788

European-Finnish (FIN) AF: 0.949 AC: 6813 AN: 7176

Middle Eastern (MID) AF: 0.988 AC: 253 AN: 256

European-Non Finnish (NFE) AF: 0.990 AC: 58448 AN: 59052

Other (OTH) AF: 0.955 AC: 1626 AN: 1702

Alfa AF: 0.958 Hom.: 5728

Asia WGS AF: 0.982 AC: 1856 AN: 1890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4860308; hg19: chr4-69489672;