ENST00000421575.6:n.208-14419C>G

Variant names:

• chr2-52747196-G-C
• rs1384918
• ENST00000421575.6:n.208-14419C>G

Variant summary

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

The ENST00000421575.6(ENSG00000228033):​n.208-14419C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,902 control chromosomes in the GnomAD database, including 27,065 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 0.59 (27065 hom., cov: 31)
• Consequence: ENSG00000228033 ENST00000421575.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

ENSG00000228033 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369165	NR_187747.1	n.172-20378C>G		intron_variant	Intron 3 of 4
LOC105369165	NR_187748.1	n.253-14419C>G		intron_variant	Intron 4 of 6
LOC105369165	NR_187749.1	n.221-20378C>G		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228033	ENST00000421575.6	n.208-14419C>G		intron_variant	Intron 3 of 5	5
ENSG00000228033	ENST00000443237.1	n.120-20378C>G		intron_variant	Intron 2 of 3	3
ENSG00000228033	ENST00000668945.1	n.220-20378C>G		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90009 AN: 151784 Hom.: 27045 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.593 AC: 90070 AN: 151902 Hom.: 27065 Cov.: 31 AF XY: 0.588 AC XY: 43669 AN XY: 74218

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.639

Alfa AF: 0.425 Hom.: 1057

Bravo AF: 0.597

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1384918; hg19: chr2-52974334;