2-48869696-C-T

Variant names:

• chr2-48869696-C-T
• rs733726
• ENST00000634588.1:n.302+60055C>T

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.302+60055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,174 control chromosomes in the GnomAD database, including 1,676 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 0.13 (1676 hom., cov: 33)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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
ENSG00000282890	ENST00000634588.1	n.302+60055C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19919 AN: 152056 Hom.: 1668 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.131 AC: 19967 AN: 152174 Hom.: 1676 Cov.: 33 AF XY: 0.132 AC XY: 9852 AN XY: 74382

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0771

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0819 Hom.: 797

Bravo AF: 0.137

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs733726; hg19: chr2-49096835;