rs17050238

Variant names:

• chr2-59566879-G-A
• rs17050238
• ENST00000412409.3:n.545+27926C>T

Variant summary

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

The ENST00000412409.3(ENSG00000233891):​n.545+27926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 152,254 control chromosomes in the GnomAD database, including 40 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 0.010 (40 hom., cov: 33)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.108 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
ENSG00000233891	ENST00000412409.3	n.545+27926C>T		intron_variant	Intron 4 of 4	3
ENSG00000271955	ENST00000606382.1	n.237-54674C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0101 AC: 1535 AN: 152138 Hom.: 40 Cov.: 33

Gnomad AFR AF: 0.00302

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0260

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00462

Gnomad OTH AF: 0.0125

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

GnomAD4 genome AF: 0.0101 AC: 1534 AN: 152254 Hom.: 40 Cov.: 33 AF XY: 0.0106 AC XY: 790 AN XY: 74438

Gnomad4 AFR AF: 0.00301

Gnomad4 AMR AF: 0.0260

Gnomad4 ASJ AF: 0.00230

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.00113

Gnomad4 NFE AF: 0.00462

Gnomad4 OTH AF: 0.0133

Alfa AF: 0.00638 Hom.: 4

Bravo AF: 0.0124

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17050238; hg19: chr2-59794014;