rs12210050

Positions:

• chr6-475489-C-T

Variant summary

Our verdict is Benign. Variant got -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: ENST00000661640.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000661640.1	n.617C>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.0316

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.145 Hom.: 3461

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12210050; hg19: chr6-475489;