2-117110281-C-T

Variant names:

• chr2-117110281-C-T
• rs332880
• ENST00000849499.1:n.126-9360G>A

Variant summary

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

The ENST00000849499.1(ENSG00000310388):​n.126-9360G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 151,840 control chromosomes in the GnomAD database, including 48,592 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 0.80 (48592 hom., cov: 29)
• Consequence: ENSG00000310388 ENST00000849499.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 1 publications found

Genes affected

ENSG00000310388 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.892 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
ENSG00000310388	ENST00000849499.1	n.126-9360G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121097 AN: 151722 Hom.: 48544 Cov.: 29

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.798 AC: 121202 AN: 151840 Hom.: 48592 Cov.: 29 AF XY: 0.803 AC XY: 59557 AN XY: 74188

African (AFR) AF: 0.780 AC: 32272 AN: 41390

American (AMR) AF: 0.869 AC: 13272 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2784 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4369 AN: 5094

South Asian (SAS) AF: 0.914 AC: 4406 AN: 4818

European-Finnish (FIN) AF: 0.761 AC: 8027 AN: 10548

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53404 AN: 67928

Other (OTH) AF: 0.785 AC: 1658 AN: 2112

Alfa AF: 0.794 Hom.: 25237

Bravo AF: 0.803

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.30
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs332880; hg19: chr2-117867857; COSMIC: COSV60099648;