4-179498463-G-C

Variant names:

• chr4-179498463-G-C
• rs1455691

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 0.407 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.333 AC: 13737 AN: 41220

American (AMR) AF: 0.451 AC: 6856 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2374 AN: 5076

South Asian (SAS) AF: 0.341 AC: 1601 AN: 4698

European-Finnish (FIN) AF: 0.493 AC: 5183 AN: 10508

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29560 AN: 67842

Other (OTH) AF: 0.405 AC: 849 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1455691; hg19: chr4-180419616;