rs1456087

chr4-27502784-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 0.659 in 151,978 control chromosomes in the GnomAD database, including 33,954 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 0.66 (33954 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.659 AC: 100116 AN: 151860 Hom.: 33915 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.659 AC: 100211 AN: 151978 Hom.: 33954 Cov.: 33 AF XY: 0.655 AC XY: 48624 AN XY: 74262

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.636

Alfa AF: 0.647 Hom.: 4627

Bravo AF: 0.679

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.6
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456087; hg19: chr4-27504406;