chr6-32689557-T-A

Variant names:

• chr6-32689557-T-A
• rs4538747
• ENST00000790899.1:n.798A>T

Variant summary

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

The ENST00000790899.1(ENSG00000302994):​n.798A>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 0.259 in 151,468 control chromosomes in the GnomAD database, including 5,358 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 0.26 (5358 hom., cov: 31)
• Consequence: ENSG00000302994 ENST00000790899.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 11 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 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.798A>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39270 AN: 151350 Hom.: 5364 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.259 AC: 39281 AN: 151468 Hom.: 5358 Cov.: 31 AF XY: 0.256 AC XY: 18938 AN XY: 73988

African (AFR) AF: 0.263 AC: 10837 AN: 41230

American (AMR) AF: 0.242 AC: 3682 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3466

East Asian (EAS) AF: 0.447 AC: 2278 AN: 5092

South Asian (SAS) AF: 0.245 AC: 1169 AN: 4762

European-Finnish (FIN) AF: 0.183 AC: 1924 AN: 10528

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17395 AN: 67888

Other (OTH) AF: 0.277 AC: 582 AN: 2100

Alfa AF: 0.173 Hom.: 383

Bravo AF: 0.263

Asia WGS AF: 0.382 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.7
DANN	Benign	0.52
PhyloP100		-0.063

Splicing

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

Other links and lift over

dbSNP: rs4538747; hg19: chr6-32657334;