ENST00000456384.1:n.268+10303G>A

Variant names:

• chr2-204485926-G-A
• rs4673300
• ENST00000456384.1:n.268+10303G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456384.1(ENSG00000237843):​n.268+10303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,744 control chromosomes in the GnomAD database, including 10,504 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 0.35 (10504 hom., cov: 32)
• Consequence: ENSG00000237843 ENST00000456384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

Genes affected

ENSG00000237843 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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
ENSG00000237843	ENST00000456384.1	n.268+10303G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52876 AN: 151624 Hom.: 10488 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.349 AC: 52922 AN: 151744 Hom.: 10504 Cov.: 32 AF XY: 0.353 AC XY: 26182 AN XY: 74170

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.367

Alfa AF: 0.360 Hom.: 17249

Bravo AF: 0.357

Asia WGS AF: 0.605 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.73
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4673300; hg19: chr2-205350649;