ENST00000798760.1:n.45-28217A>G

Variant names:

• chr2-81824988-T-C
• rs1432170
• ENST00000798760.1:n.45-28217A>G

Variant summary

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

The ENST00000798760.1(ENSG00000303999):​n.45-28217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 151,946 control chromosomes in the GnomAD database, including 43,871 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 0.76 (43871 hom., cov: 31)
• Consequence: ENSG00000303999 ENST00000798760.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 2 publications found

Genes affected

ENSG00000303999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798760.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102724542	NR_187691.1		n.498-23765T>C		intron	N/A
	LOC102724542	NR_187692.1		n.576-23765T>C		intron	N/A
	LOC102724542	NR_187693.1		n.1303+2614T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303999	ENST00000798760.1		n.45-28217A>G		intron	N/A
	ENSG00000303999	ENST00000798761.1		n.149-28217A>G		intron	N/A
	ENSG00000304018	ENST00000798887.1		n.125+2597T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115142 AN: 151828 Hom.: 43827 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.811

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.758 AC: 115241 AN: 151946 Hom.: 43871 Cov.: 31 AF XY: 0.751 AC XY: 55766 AN XY: 74258

African (AFR) AF: 0.729 AC: 30217 AN: 41440

American (AMR) AF: 0.754 AC: 11520 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3013 AN: 3468

East Asian (EAS) AF: 0.625 AC: 3220 AN: 5154

South Asian (SAS) AF: 0.694 AC: 3331 AN: 4800

European-Finnish (FIN) AF: 0.723 AC: 7621 AN: 10542

Middle Eastern (MID) AF: 0.807 AC: 234 AN: 290

European-Non Finnish (NFE) AF: 0.790 AC: 53681 AN: 67962

Other (OTH) AF: 0.757 AC: 1595 AN: 2108

Alfa AF: 0.783 Hom.: 132736

Bravo AF: 0.759

Asia WGS AF: 0.685 AC: 2382 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.39
PhyloP100		0.0

Splicing

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

Other links and lift over

dbSNP: rs1432170; hg19: chr2-82052112;