15-84741334-T-C

Variant names:

• chr15-84741334-T-C
• rs1429445
• ENST00000809681.1:n.492A>G

Variant summary

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

The ENST00000809681.1(ENSG00000285667):​n.492A>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 0.843 in 152,246 control chromosomes in the GnomAD database, including 54,584 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 0.84 (54584 hom., cov: 33)
• Consequence: ENSG00000285667 ENST00000809681.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 5 publications found

Genes affected

ENSG00000285667 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.952 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
ENSG00000285667	ENST00000809681.1	n.492A>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000285667	ENST00000809684.1	n.316A>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000285667	ENST00000648837.1	n.1630+3874A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128277 AN: 152128 Hom.: 54535 Cov.: 33

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.814

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.843 AC: 128379 AN: 152246 Hom.: 54584 Cov.: 33 AF XY: 0.839 AC XY: 62463 AN XY: 74430

African (AFR) AF: 0.959 AC: 39882 AN: 41570

American (AMR) AF: 0.757 AC: 11568 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2967 AN: 3470

East Asian (EAS) AF: 0.941 AC: 4876 AN: 5180

South Asian (SAS) AF: 0.793 AC: 3829 AN: 4828

European-Finnish (FIN) AF: 0.751 AC: 7952 AN: 10590

Middle Eastern (MID) AF: 0.824 AC: 239 AN: 290

European-Non Finnish (NFE) AF: 0.803 AC: 54585 AN: 68010

Other (OTH) AF: 0.820 AC: 1734 AN: 2114

Alfa AF: 0.830 Hom.: 8583

Bravo AF: 0.849

Asia WGS AF: 0.866 AC: 3011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1429445; hg19: chr15-85284565;