ENST00000685247.2:n.517T>A

Variant names:

• chr6-32894830-T-A
• rs3749982
• ENST00000685247.2:n.517T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685247.2(ENSG00000289047):​n.517T>A 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 0.131 in 151,790 control chromosomes in the GnomAD database, including 1,488 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 0.13 (1488 hom., cov: 32)
• Consequence: ENSG00000289047 ENST00000685247.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752

Genes affected

ENSG00000289047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100294145	NR_037177.1	n.655T>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC100294145	NR_037178.1	n.655T>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289047	ENST00000685247.2	n.517T>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000289047	ENST00000701517.1	n.532T>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000289559	ENST00000688327.2	n.-165A>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19803 AN: 151672 Hom.: 1481 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.131 AC: 19848 AN: 151790 Hom.: 1488 Cov.: 32 AF XY: 0.131 AC XY: 9727 AN XY: 74194

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0956

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.121

Alfa AF: 0.111 Hom.: 137

Bravo AF: 0.130

Asia WGS AF: 0.141 AC: 489 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3749982; hg19: chr6-32862607; COSMIC: COSV70444650;