4-126012137-G-C

Position:

• chr4-126012137-G-C

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 0.423 in 151,950 control chromosomes in the GnomAD database, including 13,719 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 0.42 (13719 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.126012137G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250149	ENST00000667497.1	n.164-4180G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64220 AN: 151832 Hom.: 13710 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.423 AC: 64269 AN: 151950 Hom.: 13719 Cov.: 31 AF XY: 0.424 AC XY: 31495 AN XY: 74262

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.426

Alfa AF: 0.276 Hom.: 677

Bravo AF: 0.424

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.066
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320267; hg19: chr4-126933292;