2-59082913-C-T

Variant names:

• chr2-59082913-C-T
• rs2192497
• ENST00000650010.1:n.1243+21063C>T

Variant summary

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

The ENST00000650010.1(ENSG00000285673):​n.1243+21063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 152,160 control chromosomes in the GnomAD database, including 48,628 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 0.79 (48628 hom., cov: 32)
• Consequence: ENSG00000285673 ENST00000650010.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

Genes affected

ENSG00000285673 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000285673	ENST00000650010.1	n.1243+21063C>T		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120489 AN: 152042 Hom.: 48579 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.793 AC: 120594 AN: 152160 Hom.: 48628 Cov.: 32 AF XY: 0.796 AC XY: 59172 AN XY: 74380

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.831

Gnomad4 FIN AF: 0.755

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.749

Alfa AF: 0.756 Hom.: 13870

Bravo AF: 0.803

Asia WGS AF: 0.896 AC: 3115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2192497; hg19: chr2-59310048;