6-33130612-G-C

Variant names:

• chr6-33130612-G-C
• rs2294479
• ENST00000782892.1:n.430-10509G>C

Variant summary

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

The ENST00000782892.1(ENSG00000291111):​n.430-10509G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 152,172 control chromosomes in the GnomAD database, including 6,038 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 0.27 (6038 hom., cov: 32)
• Consequence: ENSG00000291111 ENST00000782892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 13 publications found

Genes affected

ENSG00000291111 (HGNC:):

ENSG00000301948 (HGNC:59163):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782892.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105375021	NR_190905.1		n.*135C>G		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291111	ENST00000782892.1		n.430-10509G>C		intron	N/A
	ENSG00000291111	ENST00000782893.1		n.404-10509G>C		intron	N/A
	ENSG00000291111	ENST00000782894.1		n.229-633G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40682 AN: 152054 Hom.: 6040 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.267 AC: 40687 AN: 152172 Hom.: 6038 Cov.: 32 AF XY: 0.268 AC XY: 19919 AN XY: 74394

African (AFR) AF: 0.147 AC: 6126 AN: 41540

American (AMR) AF: 0.246 AC: 3766 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1537 AN: 3472

East Asian (EAS) AF: 0.385 AC: 1995 AN: 5180

South Asian (SAS) AF: 0.317 AC: 1525 AN: 4816

European-Finnish (FIN) AF: 0.331 AC: 3502 AN: 10574

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21434 AN: 67980

Other (OTH) AF: 0.264 AC: 558 AN: 2114

Alfa AF: 0.314 Hom.: 4304

Bravo AF: 0.254

Asia WGS AF: 0.349 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.7
DANN	Benign	0.69
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2294479;

hg19: chr6-33098389;