chr6-70608257-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000232389 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.169 AC: 5085 AN: 30148

American (AMR) AF: 0.0658 AC: 2912 AN: 44270

Ashkenazi Jewish (ASJ) AF: 0.0590 AC: 1481 AN: 25092

East Asian (EAS) AF: 0.00134 AC: 52 AN: 38828

South Asian (SAS) AF: 0.0189 AC: 1574 AN: 83264

European-Finnish (FIN) AF: 0.0993 AC: 5194 AN: 52332

Middle Eastern (MID) AF: 0.0646 AC: 248 AN: 3840

European-Non Finnish (NFE) AF: 0.131 AC: 127657 AN: 972804

Other (OTH) AF: 0.103 AC: 5641 AN: 54774

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

African (AFR) AF: 0.165 AC: 6867 AN: 41524

American (AMR) AF: 0.0924 AC: 1413 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5186

South Asian (SAS) AF: 0.0182 AC: 88 AN: 4828

European-Finnish (FIN) AF: 0.0918 AC: 973 AN: 10604

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9131 AN: 67996

Other (OTH) AF: 0.127 AC: 269 AN: 2112

Alfa AF: 0.117 Hom.: 1033

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
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9455190; hg19: chr6-71317960;