4-119932213-G-A

Position:

• chr4-119932213-G-A

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 0.131 in 151,898 control chromosomes in the GnomAD database, including 2,189 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 0.13 (2189 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19846 AN: 151782 Hom.: 2183 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.0136

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0622

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.131 AC: 19887 AN: 151898 Hom.: 2189 Cov.: 31 AF XY: 0.130 AC XY: 9644 AN XY: 74244

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.0683

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0622

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0741 Hom.: 530

Bravo AF: 0.138

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
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: rs10518344; hg19: chr4-120853368;