rs17275498

Variant names:

• chr2-230555686-A-C
• rs17275498
• ENST00000414539.1:n.293-4585T>G

Variant summary

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

The ENST00000414539.1(ENSG00000235419):​n.293-4585T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,172 control chromosomes in the GnomAD database, including 774 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 0.095 (774 hom., cov: 32)
• Consequence: ENSG00000235419 ENST00000414539.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

Genes affected

ENSG00000235419 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 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
ENSG00000235419	ENST00000414539.1	n.293-4585T>G		intron_variant	Intron 4 of 5	3
ENSG00000235419	ENST00000455357.5	n.438-4585T>G		intron_variant	Intron 5 of 6	4

Frequencies

GnomAD3 genomes AF: 0.0954 AC: 14511 AN: 152054 Hom.: 773 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.0538

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.0954 AC: 14521 AN: 152172 Hom.: 774 Cov.: 32 AF XY: 0.0928 AC XY: 6904 AN XY: 74402

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.0150

Gnomad4 SAS AF: 0.0961

Gnomad4 FIN AF: 0.0538

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.126

Alfa AF: 0.113 Hom.: 2238

Bravo AF: 0.0977

Asia WGS AF: 0.0550 AC: 192 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17275498; hg19: chr2-231420401;