ENST00000661640.1:n.617C>T

Variant names:

• chr6-475489-C-T
• rs12210050
• ENST00000661640.1:n.617C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661640.1(ENSG00000286364):​n.617C>T 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 0.107 in 152,220 control chromosomes in the GnomAD database, including 1,311 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 0.11 (1311 hom., cov: 32)
• Consequence: ENSG00000286364 ENST00000661640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 60 publications found

Genes affected

ENSG00000286364 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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
ENSG00000286364	ENST00000661640.1	n.617C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16294 AN: 152102 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0145

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.0952

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.107 AC: 16291 AN: 152220 Hom.: 1311 Cov.: 32 AF XY: 0.0994 AC XY: 7399 AN XY: 74422

African (AFR) AF: 0.0316 AC: 1311 AN: 41544

American (AMR) AF: 0.0753 AC: 1151 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4826

European-Finnish (FIN) AF: 0.112 AC: 1181 AN: 10588

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11683 AN: 67998

Other (OTH) AF: 0.0942 AC: 199 AN: 2112

Alfa AF: 0.141 Hom.: 6830

Bravo AF: 0.103

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.50
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs12210050; hg19: chr6-475489;