4-122058484-A-G

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 0.205 in 152,088 control chromosomes in the GnomAD database, including 4,602 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 0.21 (4602 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 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: 0.205 AC: 31207 AN: 151970 Hom.: 4584 Cov.: 31

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.205 AC: 31241 AN: 152088 Hom.: 4602 Cov.: 31 AF XY: 0.209 AC XY: 15513 AN XY: 74338

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.234

Alfa AF: 0.211 Hom.: 929

Bravo AF: 0.227

Asia WGS AF: 0.327 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.3
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12510683; hg19: chr4-122979639;