2-151017021-A-G

Variant names:

• chr2-151017021-A-G
• rs10497072
• ENST00000409243.1:n.299-15631T>C

Variant summary

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

The ENST00000409243.1(ENSG00000222031):​n.299-15631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,094 control chromosomes in the GnomAD database, including 58,273 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 0.87 (58273 hom., cov: 32)
• Consequence: ENSG00000222031 ENST00000409243.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 2 publications found

Genes affected

ENSG00000222031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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
ENSG00000222031	ENST00000409243.1	n.299-15631T>C		intron_variant	Intron 4 of 4	3
ENSG00000222031	ENST00000812493.1	n.181+16788T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132336 AN: 151976 Hom.: 58229 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.875

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

GnomAD4 genome AF: 0.871 AC: 132436 AN: 152094 Hom.: 58273 Cov.: 32 AF XY: 0.873 AC XY: 64905 AN XY: 74366

African (AFR) AF: 0.739 AC: 30596 AN: 41418

American (AMR) AF: 0.914 AC: 13977 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3073 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4892 AN: 5186

South Asian (SAS) AF: 0.826 AC: 3987 AN: 4824

European-Finnish (FIN) AF: 0.961 AC: 10182 AN: 10590

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62723 AN: 67996

Other (OTH) AF: 0.877 AC: 1853 AN: 2112

Alfa AF: 0.883 Hom.: 3262

Bravo AF: 0.864

Asia WGS AF: 0.878 AC: 3053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
DANN	Benign	0.50
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10497072; hg19: chr2-151873535;