chr4-181399877-T-C

Position:

• chr4-181399877-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.181399877T>C		intergenic_region
LOC124900822	XR_007058402.1	n.78-5303A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.873

Alfa AF: 0.870 Hom.: 17676

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4861952; hg19: chr4-182321030;