2-134454758-G-T

Position:

• chr2-134454758-G-T

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 0.548 in 151,962 control chromosomes in the GnomAD database, including 25,267 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 0.55 (25263 hom., cov: 31)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.94

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134454758G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83103 AN: 151812 Hom.: 25192 Cov.: 31

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.559

GnomAD4 exome AF: 0.500 AC: 15 AN: 30 Hom.: 4 AF XY: 0.500 AC XY: 12 AN XY: 24

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.548 AC: 83236 AN: 151932 Hom.: 25263 Cov.: 31 AF XY: 0.555 AC XY: 41250 AN XY: 74266

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.565

Alfa AF: 0.447 Hom.: 22625

Bravo AF: 0.577

Asia WGS AF: 0.854 AC: 2968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0040
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs539588; hg19: chr2-135212329;