7-125933854-T-G

Variant names:

• chr7-125933854-T-G
• rs10256927
• ENST00000411856.1:n.*22T>G

Variant summary

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

The ENST00000411856.1(ENSG00000197462):​n.*22T>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: ENSG00000197462 ENST00000411856.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

ENSG00000197462 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000197462	ENST00000411856.1	n.*22T>G		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;