rs284117

Positions:

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

Variant summary

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

The ENST00000426262.1(ENSG00000225006):​n.128+1665T>A variant causes a intron, non coding transcript 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: ENST00000426262.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000426262.1	n.128+1665T>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.630

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs284117; hg19: chr1-188479461;