2-48948101-T-G

Variant names:

• chr2-48948101-T-G
• rs17500266
• ENST00000634588.1:n.492+1696T>G

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.492+1696T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,046 control chromosomes in the GnomAD database, including 17,833 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 0.48 (17833 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

ENSG00000282890 (HGNC:58158):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 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.492+1696T>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72838 AN: 151928 Hom.: 17830 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.479 AC: 72864 AN: 152046 Hom.: 17833 Cov.: 32 AF XY: 0.482 AC XY: 35808 AN XY: 74334

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.488

Alfa AF: 0.506 Hom.: 36981

Bravo AF: 0.469

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17500266; hg19: chr2-49175240;