rs284117

Variant names:

• chr1-188510330-T-A
• rs284117
• ENST00000426262.1:n.128+1665T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-188510330-T-A
• chr1-188510330-T-G

Variant summary

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

The ENST00000426262.1(ENSG00000225006):​n.128+1665T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 151,458 control chromosomes in the GnomAD database, including 30,407 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 0.63 (30407 hom., cov: 30)
• Consequence: ENSG00000225006 ENST00000426262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 2 publications found

Genes affected

ENSG00000225006 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.815 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
ENSG00000225006	ENST00000426262.1	n.128+1665T>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95317 AN: 151340 Hom.: 30391 Cov.: 30

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.630 AC: 95374 AN: 151458 Hom.: 30407 Cov.: 30 AF XY: 0.629 AC XY: 46526 AN XY: 73954

African (AFR) AF: 0.715 AC: 29527 AN: 41312

American (AMR) AF: 0.594 AC: 9040 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1988 AN: 3460

East Asian (EAS) AF: 0.836 AC: 4276 AN: 5116

South Asian (SAS) AF: 0.736 AC: 3532 AN: 4802

European-Finnish (FIN) AF: 0.576 AC: 6016 AN: 10446

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 38946 AN: 67790

Other (OTH) AF: 0.630 AC: 1329 AN: 2108

Alfa AF: 0.608 Hom.: 3520

Bravo AF: 0.634

Asia WGS AF: 0.777 AC: 2698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
DANN	Benign	0.38
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs284117; hg19: chr1-188479461;