rs686015

Variant names:

• chr1-160202183-T-A
• rs686015
• ENST00000418602.2:n.*15A>T

Your query was ambiguous. Multiple possible variants found:

• chr1-160202183-T-A
• chr1-160202183-T-C

Variant summary

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

The ENST00000418602.2(ENSG00000227741):​n.*15A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,134 control chromosomes in the GnomAD database, including 10,809 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 0.35 (10808 hom., cov: 32)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: ENSG00000227741 ENST00000418602.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 7 publications found

Genes affected

ENSG00000227741 (HGNC:58221):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PEA15-AS1	NR_123725.1	n.*16A>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227741	ENST00000418602.2	n.*15A>T		downstream_gene_variant		2
ENSG00000227741	ENST00000756717.1	n.*18A>T		downstream_gene_variant
ENSG00000227741	ENST00000756718.1	n.*10A>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53303 AN: 151990 Hom.: 10813 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.358

GnomAD4 exome AF: 0.308 AC: 8 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.318 AC XY: 7 AN XY: 22

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 4 AN: 20

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.350 AC: 53307 AN: 152108 Hom.: 10808 Cov.: 32 AF XY: 0.354 AC XY: 26341 AN XY: 74360

African (AFR) AF: 0.135 AC: 5612 AN: 41524

American (AMR) AF: 0.420 AC: 6416 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3472

East Asian (EAS) AF: 0.535 AC: 2771 AN: 5178

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4701 AN: 10544

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29564 AN: 67968

Other (OTH) AF: 0.356 AC: 754 AN: 2116

Alfa AF: 0.286 Hom.: 838

Bravo AF: 0.339

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.52
PhyloP100		0.10
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs686015; hg19: chr1-160171973;