chr6-32689801-T-C

Variant names:

• chr6-32689801-T-C
• rs7774434
• ENST00000790899.1:n.554A>G

Variant summary

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

The ENST00000790899.1(ENSG00000302994):​n.554A>G 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 0.405 in 151,764 control chromosomes in the GnomAD database, including 12,819 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 0.41 (12819 hom., cov: 31)
• Consequence: ENSG00000302994 ENST00000790899.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 74 publications found

Genes affected

ENSG00000302994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 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
ENSG00000302994	ENST00000790899.1	n.554A>G		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61401 AN: 151646 Hom.: 12805 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.405 AC: 61465 AN: 151764 Hom.: 12819 Cov.: 31 AF XY: 0.413 AC XY: 30582 AN XY: 74126

African (AFR) AF: 0.379 AC: 15661 AN: 41360

American (AMR) AF: 0.506 AC: 7716 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2112 AN: 5130

South Asian (SAS) AF: 0.519 AC: 2498 AN: 4810

European-Finnish (FIN) AF: 0.481 AC: 5037 AN: 10480

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25291 AN: 67956

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.392 Hom.: 39321

Bravo AF: 0.410

Asia WGS AF: 0.450 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.4
DANN	Benign	0.39
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7774434; hg19: chr6-32657578;