6-27122625-C-T

Position:

• chr6-27122625-C-T

Variant summary

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

The 6-27122625-C-T 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: ENST00000607175.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000607175.1			downstream_gene_variant

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;