ENST00000421575.7:n.240-1492G>A

Variant names:

• chr2-52734269-C-T
• rs1840321
• ENST00000421575.7:n.240-1492G>A

Variant summary

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

The ENST00000421575.7(ENSG00000228033):​n.240-1492G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 152,038 control chromosomes in the GnomAD database, including 27,441 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 0.60 (27441 hom., cov: 32)
• Consequence: ENSG00000228033 ENST00000421575.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.970
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 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.172-7451G>A		intron	N/A
	LOC105369165	NR_187748.1		n.253-1492G>A		intron	N/A
	LOC105369165	NR_187749.1		n.221-7451G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228033	ENST00000421575.7	TSL:5	n.240-1492G>A		intron	N/A
	ENSG00000228033	ENST00000443237.2	TSL:3	n.185-7451G>A		intron	N/A
	ENSG00000228033	ENST00000668945.1		n.220-7451G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90586 AN: 151918 Hom.: 27416 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.596 AC: 90655 AN: 152038 Hom.: 27441 Cov.: 32 AF XY: 0.592 AC XY: 44033 AN XY: 74340

African (AFR) AF: 0.629 AC: 26068 AN: 41458

American (AMR) AF: 0.589 AC: 8993 AN: 15266

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

East Asian (EAS) AF: 0.443 AC: 2281 AN: 5152

South Asian (SAS) AF: 0.547 AC: 2640 AN: 4822

European-Finnish (FIN) AF: 0.534 AC: 5648 AN: 10584

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40692 AN: 67968

Other (OTH) AF: 0.634 AC: 1340 AN: 2114

Alfa AF: 0.581 Hom.: 3238

Bravo AF: 0.600

Asia WGS AF: 0.504 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.37
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1840321; hg19: chr2-52961407;