chr1-172909883-T-C

Variant names:

• chr1-172909883-T-C
• rs2227203
• ENST00000432694.2:n.224-94399T>C

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.224-94399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,040 control chromosomes in the GnomAD database, including 39,029 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 0.70 (39029 hom., cov: 31)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 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.224-94399T>C		intron_variant	Intron 1 of 4	3
ENSG00000224000	ENST00000717047.1	n.571+2631T>C		intron_variant	Intron 4 of 4
ENSG00000224000	ENST00000717048.1	n.323+26184T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106129 AN: 151922 Hom.: 38975 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.699 AC: 106241 AN: 152040 Hom.: 39029 Cov.: 31 AF XY: 0.704 AC XY: 52347 AN XY: 74312

African (AFR) AF: 0.915 AC: 37981 AN: 41494

American (AMR) AF: 0.727 AC: 11107 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2257 AN: 3470

East Asian (EAS) AF: 0.921 AC: 4753 AN: 5162

South Asian (SAS) AF: 0.751 AC: 3603 AN: 4800

European-Finnish (FIN) AF: 0.607 AC: 6415 AN: 10560

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37898 AN: 67970

Other (OTH) AF: 0.689 AC: 1453 AN: 2110

Alfa AF: 0.612 Hom.: 50182

Bravo AF: 0.723

Asia WGS AF: 0.794 AC: 2765 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2227203; hg19: chr1-172879023;