1-22000388-T-G

Variant names:

• chr1-22000388-T-G
• rs4532803
• ENST00000650360.1:n.522-5059T>G

Variant summary

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

The ENST00000650360.1(ENSG00000285959):​n.522-5059T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 149,940 control chromosomes in the GnomAD database, including 18,925 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 0.47 (18925 hom., cov: 30)
• Consequence: ENSG00000285959 ENST00000650360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 1 publications found

Genes affected

ENSG00000285959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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
ENSG00000285959	ENST00000650360.1	n.522-5059T>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.466 AC: 69848 AN: 149822 Hom.: 18890 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.466 AC: 69930 AN: 149940 Hom.: 18925 Cov.: 30 AF XY: 0.469 AC XY: 34337 AN XY: 73166

African (AFR) AF: 0.676 AC: 27231 AN: 40258

American (AMR) AF: 0.511 AC: 7705 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1078 AN: 3458

East Asian (EAS) AF: 0.662 AC: 3328 AN: 5030

South Asian (SAS) AF: 0.402 AC: 1913 AN: 4764

European-Finnish (FIN) AF: 0.427 AC: 4453 AN: 10430

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22842 AN: 67620

Other (OTH) AF: 0.432 AC: 903 AN: 2090

Alfa AF: 0.407 Hom.: 1833

Bravo AF: 0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4532803; hg19: chr1-22326881;