6-160698207-C-T

Variant names:

• chr6-160698207-C-T
• rs783144
• ENST00000448126.5:n.-81C>T

Variant summary

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

The ENST00000448126.5(ENSG00000224477):​n.-81C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,136 control chromosomes in the GnomAD database, including 6,328 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 0.26 (6327 hom., cov: 31)
  • Exomes 𝑓: 0.22 (1 hom.)
• Consequence: ENSG00000224477 ENST00000448126.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

ENSG00000224477 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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
ENSG00000224477	ENST00000448126.5	n.-81C>T		upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.263 AC: 40044 AN: 151986 Hom.: 6329 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.219 AC: 7 AN: 32 Hom.: 1 AF XY: 0.192 AC XY: 5 AN XY: 26

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.233

GnomAD4 genome AF: 0.263 AC: 40049 AN: 152104 Hom.: 6327 Cov.: 31 AF XY: 0.270 AC XY: 20103 AN XY: 74338

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.272

Alfa AF: 0.166 Hom.: 373

Bravo AF: 0.270

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs783144; hg19: chr6-161119239; COSMIC: COSV51981736;