2-30040752-A-G

Variant names:

• chr2-30040752-A-G
• rs718153
• ENST00000717100.1:n.354-51633T>C

Variant summary

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

The ENST00000717100.1(ENSG00000233862):​n.354-51633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,140 control chromosomes in the GnomAD database, including 46,209 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 0.77 (46209 hom., cov: 32)
• Consequence: ENSG00000233862 ENST00000717100.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 2 publications found

Genes affected

ENSG00000233862 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) 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
ENSG00000233862	ENST00000717100.1	n.354-51633T>C		intron_variant	Intron 2 of 5
ENSG00000233862	ENST00000717101.1	n.443+79016T>C		intron_variant	Intron 4 of 4
ENSG00000233862	ENST00000769926.1	n.393+79016T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117348 AN: 152020 Hom.: 46147 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.772 AC: 117468 AN: 152140 Hom.: 46209 Cov.: 32 AF XY: 0.774 AC XY: 57574 AN XY: 74356

African (AFR) AF: 0.906 AC: 37596 AN: 41510

American (AMR) AF: 0.811 AC: 12408 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4685 AN: 5184

South Asian (SAS) AF: 0.828 AC: 3984 AN: 4814

European-Finnish (FIN) AF: 0.696 AC: 7355 AN: 10570

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.687 AC: 46726 AN: 67986

Other (OTH) AF: 0.743 AC: 1569 AN: 2112

Alfa AF: 0.736 Hom.: 44481

Bravo AF: 0.787

Asia WGS AF: 0.861 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs718153; hg19: chr2-30263618;