rs1870481

Variant names:

• chr4-117741865-C-T
• rs1870481

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;