1-82296726-T-C

Variant names:

• chr1-82296726-T-C
• rs996725
• ENST00000650063.1:n.888-80954A>G

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.888-80954A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 151,944 control chromosomes in the GnomAD database, including 29,919 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 (29919 hom., cov: 31)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 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.888-80954A>G		intron_variant	Intron 6 of 6
ENSG00000233290	ENST00000653483.1	n.720-80954A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94937 AN: 151826 Hom.: 29876 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.625 AC: 95040 AN: 151944 Hom.: 29919 Cov.: 31 AF XY: 0.619 AC XY: 45957 AN XY: 74264

African (AFR) AF: 0.602 AC: 24931 AN: 41398

American (AMR) AF: 0.654 AC: 9984 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2414 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3919 AN: 5154

South Asian (SAS) AF: 0.539 AC: 2598 AN: 4820

European-Finnish (FIN) AF: 0.539 AC: 5687 AN: 10542

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43186 AN: 67972

Other (OTH) AF: 0.661 AC: 1394 AN: 2110

Alfa AF: 0.610 Hom.: 3520

Bravo AF: 0.634

Asia WGS AF: 0.632 AC: 2197 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	0.28
DANN	Benign	0.62
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs996725; hg19: chr1-82762409;