rs4861952

Variant names:

• chr4-181399877-T-C
• rs4861952
• XR_007058402.1:n.78-5303A>G

Variant summary

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

The XR_007058402.1(LOC124900822):​n.78-5303A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,242 control chromosomes in the GnomAD database, including 56,645 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 0.86 (56645 hom., cov: 33)
• Consequence: LOC124900822 XR_007058402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 2 publications found

Genes affected

LOC124900822 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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: 0.862 AC: 131102 AN: 152124 Hom.: 56605 Cov.: 33

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.862 AC: 131198 AN: 152242 Hom.: 56645 Cov.: 33 AF XY: 0.865 AC XY: 64408 AN XY: 74432

African (AFR) AF: 0.815 AC: 33838 AN: 41532

American (AMR) AF: 0.908 AC: 13884 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3025 AN: 3472

East Asian (EAS) AF: 0.952 AC: 4937 AN: 5186

South Asian (SAS) AF: 0.876 AC: 4221 AN: 4820

European-Finnish (FIN) AF: 0.882 AC: 9351 AN: 10604

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59065 AN: 68022

Other (OTH) AF: 0.873 AC: 1847 AN: 2116

Alfa AF: 0.868 Hom.: 31762

Bravo AF: 0.861

Asia WGS AF: 0.902 AC: 3132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.31
DANN	Benign	0.72
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs4861952; hg19: chr4-182321030;