2-480776-T-C

Variant names:

• chr2-480776-T-C
• rs907302
• ENST00000720259.1:n.107+808A>G

Variant summary

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

The ENST00000720259.1(ENSG00000293968):​n.107+808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,060 control chromosomes in the GnomAD database, including 27,691 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 0.60 (27691 hom., cov: 33)
• Consequence: ENSG00000293968 ENST00000720259.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 5 publications found

Genes affected

ENSG00000293968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720259.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293968	ENST00000720259.1		n.107+808A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90995 AN: 151942 Hom.: 27657 Cov.: 33

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.599 AC: 91076 AN: 152060 Hom.: 27691 Cov.: 33 AF XY: 0.606 AC XY: 45072 AN XY: 74332

African (AFR) AF: 0.589 AC: 24419 AN: 41460

American (AMR) AF: 0.703 AC: 10753 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1953 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4640 AN: 5168

South Asian (SAS) AF: 0.657 AC: 3166 AN: 4818

European-Finnish (FIN) AF: 0.589 AC: 6231 AN: 10574

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37947 AN: 67964

Other (OTH) AF: 0.610 AC: 1287 AN: 2110

Alfa AF: 0.573 Hom.: 4133

Bravo AF: 0.611

Asia WGS AF: 0.777 AC: 2704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.30
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs907302; hg19: chr2-480776;