6-25054937-T-G

Position:

• chr6-25054937-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 0.575 in 152,028 control chromosomes in the GnomAD database, including 26,817 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 0.57 (26815 hom., cov: 32)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.25054937T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000223623	ENST00000416595.1	n.63-388A>C		intron_variant		3
ENSG00000229313	ENST00000428903.1	n.79-26T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87328 AN: 151906 Hom.: 26804 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.575 AC: 87366 AN: 152024 Hom.: 26815 Cov.: 32 AF XY: 0.578 AC XY: 42922 AN XY: 74310

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.673

Gnomad4 OTH AF: 0.568

Alfa AF: 0.648 Hom.: 66708

Bravo AF: 0.553

Asia WGS AF: 0.690 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs458664; hg19: chr6-25055165;