ENST00000701517.1:n.1990G>A

Variant names:

• chr6-32902280-G-A
• rs3101942
• ENST00000701517.1:n.1990G>A

Variant summary

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

The ENST00000701517.1(ENSG00000289047):​n.1990G>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 0.67 in 152,010 control chromosomes in the GnomAD database, including 35,439 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 0.67 (35439 hom., cov: 32)
• Consequence: ENSG00000289047 ENST00000701517.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

Genes affected

ENSG00000289047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100294145	NR_037177.1	n.2212G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC100294145	NR_037178.1	n.2113G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289047	ENST00000701517.1	n.1990G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000289047	ENST00000685247.2	n.*120G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101686 AN: 151892 Hom.: 35381 Cov.: 32

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.670 AC: 101801 AN: 152010 Hom.: 35439 Cov.: 32 AF XY: 0.662 AC XY: 49139 AN XY: 74270

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.694

Alfa AF: 0.612 Hom.: 26926

Bravo AF: 0.688

Asia WGS AF: 0.616 AC: 2132 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.12
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3101942; hg19: chr6-32870057;