1-82589116-C-T

Variant names:

• chr1-82589116-C-T
• rs10874322
• ENST00000650063.1:n.475-33555G>A

Variant summary

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

The ENST00000650063.1(ENSG00000233290):​n.475-33555G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,978 control chromosomes in the GnomAD database, including 1,427 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 0.14 (1427 hom., cov: 32)
• Consequence: ENSG00000233290 ENST00000650063.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• 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=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 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.475-33555G>A		intron_variant	Intron 5 of 6
ENSG00000233290	ENST00000653483.1	n.307-33555G>A		intron_variant	Intron 3 of 4
ENSG00000233290	ENST00000663002.2	n.167-33555G>A		intron_variant	Intron 2 of 3
ENSG00000233290	ENST00000702694.1	n.167-33555G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20713 AN: 151860 Hom.: 1421 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.136 AC: 20739 AN: 151978 Hom.: 1427 Cov.: 32 AF XY: 0.139 AC XY: 10309 AN XY: 74262

African (AFR) AF: 0.169 AC: 7016 AN: 41450

American (AMR) AF: 0.0971 AC: 1484 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 605 AN: 3470

East Asian (EAS) AF: 0.123 AC: 631 AN: 5140

South Asian (SAS) AF: 0.205 AC: 987 AN: 4816

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10564

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.121 AC: 8212 AN: 67950

Other (OTH) AF: 0.126 AC: 265 AN: 2106

Alfa AF: 0.123 Hom.: 3220

Bravo AF: 0.133

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	16
DANN	Benign	0.53
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10874322; hg19: chr1-83054799;