2-52747196-G-C

Variant names:

• chr2-52747196-G-C
• rs1384918
• ENST00000421575.7:n.240-14419C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421575.7(ENSG00000228033):​n.240-14419C>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 ENST00000421575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 4 publications found

Genes affected

ENSG00000228033 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421575.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369165	NR_187747.1		n.172-20378C>G		intron	N/A
	LOC105369165	NR_187748.1		n.253-14419C>G		intron	N/A
	LOC105369165	NR_187749.1		n.221-20378C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228033	ENST00000421575.7	TSL:5	n.240-14419C>G		intron	N/A
	ENSG00000228033	ENST00000443237.2	TSL:3	n.185-20378C>G		intron	N/A
	ENSG00000228033	ENST00000668945.1		n.220-20378C>G		intron	N/A

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

African (AFR) AF: 0.618 AC: 25606 AN: 41450

American (AMR) AF: 0.585 AC: 8924 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2062 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2324 AN: 5124

South Asian (SAS) AF: 0.528 AC: 2529 AN: 4794

European-Finnish (FIN) AF: 0.534 AC: 5642 AN: 10558

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40700 AN: 67942

Other (OTH) AF: 0.639 AC: 1349 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.39
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1384918; hg19: chr2-52974334;