6-33029897-T-C

Variant names:

• chr6-33029897-T-C
• rs6920606
• ENST00000722275.1:n.223T>C

Variant summary

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

The ENST00000722275.1(ENSG00000294261):​n.223T>C 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 0.477 in 151,934 control chromosomes in the GnomAD database, including 17,629 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 0.48 (17629 hom., cov: 31)
• Consequence: ENSG00000294261 ENST00000722275.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 27 publications found

Genes affected

ENSG00000294261 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.677 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
ENSG00000294261	ENST00000722275.1	n.223T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72421 AN: 151814 Hom.: 17601 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.477 AC: 72481 AN: 151934 Hom.: 17629 Cov.: 31 AF XY: 0.486 AC XY: 36107 AN XY: 74256

African (AFR) AF: 0.449 AC: 18609 AN: 41414

American (AMR) AF: 0.428 AC: 6540 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3468

East Asian (EAS) AF: 0.550 AC: 2838 AN: 5162

South Asian (SAS) AF: 0.696 AC: 3347 AN: 4806

European-Finnish (FIN) AF: 0.551 AC: 5815 AN: 10548

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31382 AN: 67938

Other (OTH) AF: 0.487 AC: 1027 AN: 2108

Alfa AF: 0.467 Hom.: 67940

Bravo AF: 0.460

Asia WGS AF: 0.639 AC: 2221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.37
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6920606; hg19: chr6-32997674;