7-125933854-T-G

Position:

• chr7-125933854-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 7-125933854-T-G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,878 control chromosomes in the GnomAD database, including 42,172 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 0.74 (42171 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENST00000411856.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000411856.1			downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112911 AN: 151758 Hom.: 42146 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.766

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.744 AC: 112980 AN: 151876 Hom.: 42171 Cov.: 32 AF XY: 0.743 AC XY: 55131 AN XY: 74236

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.764

Alfa AF: 0.756 Hom.: 21835

Bravo AF: 0.750

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.23
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10256927; hg19: chr7-125573908;