6-25054937-T-G

Variant names:

• chr6-25054937-T-G
• rs458664
• ENST00000416595.1:n.63-388A>C

Variant summary

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

The ENST00000416595.1(ENSG00000223623):​n.63-388A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000223623 ENST00000416595.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.423

Genes affected

ENSG00000223623 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223623	ENST00000416595.1	n.63-388A>C		intron_variant	Intron 1 of 3	3
ENSG00000229313	ENST00000428903.1	n.79-26T>G		intron_variant	Intron 1 of 2	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;