chr4-122600025-A-G

Position:

• chr4-122600025-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 0.412 in 151,782 control chromosomes in the GnomAD database, including 13,108 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 (13108 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.412 AC: 62523 AN: 151664 Hom.: 13093 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.412 AC: 62579 AN: 151782 Hom.: 13108 Cov.: 31 AF XY: 0.406 AC XY: 30084 AN XY: 74160

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.399

Alfa AF: 0.409 Hom.: 26609

Bravo AF: 0.425

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs975405; hg19: chr4-123521180;