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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900822	XR_007058402.1	n.78-5303A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;