1-82282893-T-C

Variant names:

• chr1-82282893-T-C
• rs785627
• ENST00000650063.1:n.888-67121A>G

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.888-67121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 151,950 control chromosomes in the GnomAD database, including 45,491 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 0.77 (45491 hom., cov: 31)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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
ENSG00000233290	ENST00000650063.1	n.888-67121A>G		intron_variant	Intron 6 of 6
ENSG00000233290	ENST00000653483.1	n.720-67121A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116783 AN: 151834 Hom.: 45467 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.769 AC: 116851 AN: 151950 Hom.: 45491 Cov.: 31 AF XY: 0.769 AC XY: 57101 AN XY: 74246

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.789

Alfa AF: 0.804 Hom.: 67325

Bravo AF: 0.761

Asia WGS AF: 0.882 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs785627; hg19: chr1-82748577;