chr1-172929262-G-A

Variant names:

• chr1-172929262-G-A
• rs12037606
• ENST00000432694.2:n.224-75020G>A

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.224-75020G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 151,730 control chromosomes in the GnomAD database, including 22,349 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 0.53 (22349 hom., cov: 33)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 11 publications found

Genes affected

ENSG00000224000 (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 = 0.898 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
ENSG00000224000	ENST00000432694.2	n.224-75020G>A		intron_variant	Intron 1 of 4	3
ENSG00000224000	ENST00000717048.1	n.323+45563G>A		intron_variant	Intron 2 of 2
ENSG00000294781	ENST00000725977.1	n.229+4239C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79629 AN: 151612 Hom.: 22325 Cov.: 33

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.525 AC: 79705 AN: 151730 Hom.: 22349 Cov.: 33 AF XY: 0.536 AC XY: 39757 AN XY: 74134

African (AFR) AF: 0.646 AC: 26667 AN: 41304

American (AMR) AF: 0.605 AC: 9237 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1679 AN: 3466

East Asian (EAS) AF: 0.919 AC: 4761 AN: 5178

South Asian (SAS) AF: 0.643 AC: 3096 AN: 4818

European-Finnish (FIN) AF: 0.503 AC: 5279 AN: 10488

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27406 AN: 67904

Other (OTH) AF: 0.528 AC: 1115 AN: 2110

Alfa AF: 0.469 Hom.: 35637

Bravo AF: 0.544

Asia WGS AF: 0.727 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.41
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs12037606; hg19: chr1-172898402;