rs1870481

chr4-117741865-C-T

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 0.544 in 152,044 control chromosomes in the GnomAD database, including 24,269 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 0.54 (24269 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82544 AN: 151926 Hom.: 24228 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.544 AC: 82644 AN: 152044 Hom.: 24269 Cov.: 33 AF XY: 0.542 AC XY: 40276 AN XY: 74312

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.552

Alfa AF: 0.502 Hom.: 4700

Bravo AF: 0.569

Asia WGS AF: 0.517 AC: 1794 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.31
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870481; hg19: chr4-118663020;