rs4478239

chr4-187270152-C-Achr4-187270152-C-Gchr4-187270152-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 0.903 in 150,898 control chromosomes in the GnomAD database, including 61,582 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 0.90 (61582 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.903 AC: 136145 AN: 150782 Hom.: 61529 Cov.: 26

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.901

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.903 AC: 136256 AN: 150898 Hom.: 61582 Cov.: 26 AF XY: 0.901 AC XY: 66239 AN XY: 73544

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.901

Alfa AF: 0.894 Hom.: 61488

Bravo AF: 0.908

Asia WGS AF: 0.923 AC: 3198 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.65
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4478239; hg19: chr4-188191306;