chr1-58599895-A-T

Variant names:

• chr1-58599895-A-T
• rs107399
• ENST00000637377.2:n.161+23519A>T

Variant summary

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

The ENST00000767021.1(ENSG00000283445):​n.188+23519A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 150,930 control chromosomes in the GnomAD database, including 17,955 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 (17955 hom., cov: 30)
• Consequence: ENSG00000283445 ENST00000767021.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 0 publications found

Genes affected

ENSG00000283445 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767021.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283445	ENST00000637377.2	TSL:5	n.161+23519A>T		intron	N/A
	ENSG00000283445	ENST00000767021.1		n.188+23519A>T		intron	N/A
	ENSG00000283445	ENST00000767022.1		n.142+23519A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71216 AN: 150818 Hom.: 17935 Cov.: 30

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.472 AC: 71278 AN: 150930 Hom.: 17955 Cov.: 30 AF XY: 0.476 AC XY: 35037 AN XY: 73662

African (AFR) AF: 0.640 AC: 26379 AN: 41226

American (AMR) AF: 0.491 AC: 7441 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1260 AN: 3466

East Asian (EAS) AF: 0.512 AC: 2632 AN: 5140

South Asian (SAS) AF: 0.420 AC: 2013 AN: 4794

European-Finnish (FIN) AF: 0.492 AC: 4964 AN: 10084

Middle Eastern (MID) AF: 0.271 AC: 78 AN: 288

European-Non Finnish (NFE) AF: 0.375 AC: 25450 AN: 67780

Other (OTH) AF: 0.429 AC: 890 AN: 2076

Alfa AF: 0.285 Hom.: 703

Bravo AF: 0.478

Asia WGS AF: 0.538 AC: 1864 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.80
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs107399; hg19: chr1-59065567;