6-70608257-C-T

Variant names:

• chr6-70608257-C-T
• rs9455190
• ENST00000454078.1:n.1078G>A

Variant summary

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

The ENST00000454078.1(ENSG00000232389):​n.1078G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,457,566 control chromosomes in the GnomAD database, including 11,050 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 0.13 (1299 hom., cov: 32)
  • Exomes 𝑓: 0.11 (9751 hom.)
• Consequence: ENSG00000232389 ENST00000454078.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

Genes affected

ENSG00000232389 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC642590		n.70608257C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232389	ENST00000454078.1	n.1078G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19067 AN: 152096 Hom.: 1296 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0918

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.115 AC: 149844 AN: 1305352 Hom.: 9751 Cov.: 25 AF XY: 0.112 AC XY: 73243 AN XY: 656572

Gnomad4 AFR exome AF: 0.169

Gnomad4 AMR exome AF: 0.0658

Gnomad4 ASJ exome AF: 0.0590

Gnomad4 EAS exome AF: 0.00134

Gnomad4 SAS exome AF: 0.0189

Gnomad4 FIN exome AF: 0.0993

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.125 AC: 19083 AN: 152214 Hom.: 1299 Cov.: 32 AF XY: 0.121 AC XY: 9010 AN XY: 74426

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0182

Gnomad4 FIN AF: 0.0918

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.127

Alfa AF: 0.114 Hom.: 781

Bravo AF: 0.129

Asia WGS AF: 0.0270 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	9.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9455190; hg19: chr6-71317960;