chr2-114223390-G-T

Variant names:

• chr2-114223390-G-T
• rs3105491
• ENST00000801755.1:n.251+30317G>T

Variant summary

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

The ENST00000801755.1(ENSG00000304278):​n.251+30317G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,488 control chromosomes in the GnomAD database, including 30,049 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 0.61 (30049 hom., cov: 32)
• Consequence: ENSG00000304278 ENST00000801755.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.503
• Publications: 3 publications found

Genes affected

ENSG00000304278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.72 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
ENSG00000304278	ENST00000801755.1	n.251+30317G>T		intron_variant	Intron 2 of 2
ENSG00000304278	ENST00000801756.1	n.228+30317G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91770 AN: 151372 Hom.: 30040 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.606 AC: 91802 AN: 151488 Hom.: 30049 Cov.: 32 AF XY: 0.606 AC XY: 44903 AN XY: 74042

African (AFR) AF: 0.331 AC: 13633 AN: 41218

American (AMR) AF: 0.689 AC: 10505 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2358 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3597 AN: 5148

South Asian (SAS) AF: 0.626 AC: 3009 AN: 4808

European-Finnish (FIN) AF: 0.691 AC: 7199 AN: 10412

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.725 AC: 49237 AN: 67890

Other (OTH) AF: 0.638 AC: 1341 AN: 2102

Alfa AF: 0.675 Hom.: 15841

Bravo AF: 0.595

Asia WGS AF: 0.654 AC: 2238 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.60
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs3105491; hg19: chr2-114980967;