4-27502784-C-T

Variant names:

• chr4-27502784-C-T
• rs1456087

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.816 AC: 33890 AN: 41522

American (AMR) AF: 0.696 AC: 10629 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2825 AN: 5136

South Asian (SAS) AF: 0.446 AC: 2147 AN: 4818

European-Finnish (FIN) AF: 0.602 AC: 6344 AN: 10536

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40057 AN: 67908

Other (OTH) AF: 0.636 AC: 1345 AN: 2116

Alfa AF: 0.653 Hom.: 4891

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
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1456087; hg19: chr4-27504406;