6-27122625-C-T

Variant names:

• chr6-27122625-C-T
• rs7745603
• ENST00000607175.1:n.*32G>A

Variant summary

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

The ENST00000607175.1(ENSG00000272468):​n.*32G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,882 control chromosomes in the GnomAD database, including 7,254 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 0.29 (7254 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000272468 ENST00000607175.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

Genes affected

ENSG00000272468 (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 (AFR) allele frequency at 95% confidence interval = 0.461 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
ENSG00000272468	ENST00000607175.1	n.*32G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43284 AN: 151762 Hom.: 7234 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.272

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.285 AC: 43332 AN: 151880 Hom.: 7254 Cov.: 32 AF XY: 0.279 AC XY: 20728 AN XY: 74254

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.269

Alfa AF: 0.223 Hom.: 8943

Bravo AF: 0.301

Asia WGS AF: 0.194 AC: 674 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	0.57
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7745603; hg19: chr6-27090404;