ENST00000803130.1:n.214-11721G>C

Variant names:

• chr2-226617697-C-G
• rs1273819
• ENST00000803130.1:n.214-11721G>C

Variant summary

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

The ENST00000803130.1(ENSG00000304396):​n.214-11721G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,028 control chromosomes in the GnomAD database, including 23,157 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 0.53 (23157 hom., cov: 32)
• Consequence: ENSG00000304396 ENST00000803130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 6 publications found

Genes affected

ENSG00000304396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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
ENSG00000304396	ENST00000803130.1	n.214-11721G>C		intron_variant	Intron 1 of 3
ENSG00000304396	ENST00000803131.1	n.218-16325G>C		intron_variant	Intron 1 of 2
ENSG00000304396	ENST00000803132.1	n.216-11721G>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80603 AN: 151910 Hom.: 23151 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.530 AC: 80633 AN: 152028 Hom.: 23157 Cov.: 32 AF XY: 0.537 AC XY: 39869 AN XY: 74308

African (AFR) AF: 0.288 AC: 11943 AN: 41484

American (AMR) AF: 0.613 AC: 9361 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3466

East Asian (EAS) AF: 0.713 AC: 3671 AN: 5152

South Asian (SAS) AF: 0.698 AC: 3363 AN: 4816

European-Finnish (FIN) AF: 0.670 AC: 7073 AN: 10556

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41418 AN: 67952

Other (OTH) AF: 0.547 AC: 1158 AN: 2116

Alfa AF: 0.437 Hom.: 1311

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1273819; hg19: chr2-227482413;