5-126866468-T-G

Position:

• chr5-126866468-T-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 0.758 in 152,016 control chromosomes in the GnomAD database, including 44,837 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 0.76 (44837 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.126866468T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115110 AN: 151898 Hom.: 44770 Cov.: 30

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.758 AC: 115241 AN: 152016 Hom.: 44837 Cov.: 30 AF XY: 0.751 AC XY: 55747 AN XY: 74272

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.756

Alfa AF: 0.699 Hom.: 26613

Bravo AF: 0.783

Asia WGS AF: 0.671 AC: 2335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.56
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7738021; hg19: chr5-126202160;