ENST00000837382.1:n.432A>T

Variant names:

• chr6-1135704-T-A
• rs1029047
• ENST00000837382.1:n.432A>T

Variant summary

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

The ENST00000837382.1(ENSG00000289842):​n.432A>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 0.405 in 151,454 control chromosomes in the GnomAD database, including 13,246 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 0.40 (13246 hom., cov: 31)
• Consequence: ENSG00000289842 ENST00000837382.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61
• Publications: 12 publications found

Genes affected

ENSG00000289842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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
ENSG00000289842	ENST00000837382.1	n.432A>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61272 AN: 151332 Hom.: 13225 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.405 AC: 61320 AN: 151454 Hom.: 13246 Cov.: 31 AF XY: 0.401 AC XY: 29705 AN XY: 74002

African (AFR) AF: 0.560 AC: 23069 AN: 41224

American (AMR) AF: 0.302 AC: 4594 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1533 AN: 3456

East Asian (EAS) AF: 0.295 AC: 1523 AN: 5164

South Asian (SAS) AF: 0.434 AC: 2079 AN: 4786

European-Finnish (FIN) AF: 0.296 AC: 3090 AN: 10448

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24102 AN: 67840

Other (OTH) AF: 0.413 AC: 870 AN: 2108

Alfa AF: 0.200 Hom.: 352

Bravo AF: 0.408

Asia WGS AF: 0.377 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.89
DANN	Benign	0.099
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1029047; hg19: chr6-1135939;