chr7-134439253-C-T

Position:

• chr7-134439253-C-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 0.777 in 151,872 control chromosomes in the GnomAD database, including 45,939 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 0.78 (45939 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.134439253C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117919 AN: 151754 Hom.: 45896 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.777 AC: 118018 AN: 151872 Hom.: 45939 Cov.: 32 AF XY: 0.781 AC XY: 57988 AN XY: 74238

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.829

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.763

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.760

Alfa AF: 0.768 Hom.: 56984

Bravo AF: 0.782

Asia WGS AF: 0.874 AC: 3040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1708414; hg19: chr7-134124005;