1-82282893-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000233290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650063.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233290	ENST00000650063.1		n.888-67121A>G		intron	N/A
	ENSG00000233290	ENST00000653483.1		n.720-67121A>G		intron	N/A

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

African (AFR) AF: 0.652 AC: 26994 AN: 41428

American (AMR) AF: 0.778 AC: 11878 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2813 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4852 AN: 5138

South Asian (SAS) AF: 0.889 AC: 4282 AN: 4814

European-Finnish (FIN) AF: 0.761 AC: 8049 AN: 10570

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55232 AN: 67956

Other (OTH) AF: 0.789 AC: 1658 AN: 2102

Alfa AF: 0.797 Hom.: 147923

Bravo AF: 0.761

Asia WGS AF: 0.882 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs785627;

hg19: chr1-82748577;