rs2206030

Variant names:

• chr6-35436577-T-C
• rs2206030
• ENST00000794874.1:n.-96T>C

Variant summary

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

The ENST00000794874.1(ENSG00000303476):​n.-96T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,182 control chromosomes in the GnomAD database, including 32,572 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 0.63 (32572 hom., cov: 34)
• Consequence: ENSG00000303476 ENST00000794874.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 12 publications found

Genes affected

ENSG00000303476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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
ENSG00000303476	ENST00000794874.1	n.-96T>C		upstream_gene_variant
ENSG00000303476	ENST00000794875.1	n.-113T>C		upstream_gene_variant
ENSG00000303476	ENST00000794876.1	n.-113T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96044 AN: 152066 Hom.: 32546 Cov.: 34

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.631 AC: 96097 AN: 152182 Hom.: 32572 Cov.: 34 AF XY: 0.633 AC XY: 47097 AN XY: 74400

African (AFR) AF: 0.384 AC: 15948 AN: 41508

American (AMR) AF: 0.704 AC: 10766 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3470

East Asian (EAS) AF: 0.432 AC: 2234 AN: 5172

South Asian (SAS) AF: 0.677 AC: 3271 AN: 4834

European-Finnish (FIN) AF: 0.814 AC: 8634 AN: 10606

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51254 AN: 67984

Other (OTH) AF: 0.610 AC: 1288 AN: 2112

Alfa AF: 0.702 Hom.: 4872

Bravo AF: 0.611

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.40
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2206030; hg19: chr6-35404354;