4-179498463-G-C

Variant names:

• chr4-179498463-G-C
• rs1455691

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 0.407 in 151,322 control chromosomes in the GnomAD database, including 12,768 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 0.41 (12768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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: 0.407 AC: 61513 AN: 151184 Hom.: 12759 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.407 AC: 61550 AN: 151322 Hom.: 12768 Cov.: 32 AF XY: 0.407 AC XY: 30077 AN XY: 73952

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.405

Alfa AF: 0.280 Hom.: 712

Bravo AF: 0.401

Asia WGS AF: 0.378 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1455691; hg19: chr4-180419616;