chr2-52741891-G-A

Variant names:

• chr2-52741891-G-A
• rs1319797
• ENST00000421575.7:n.240-9114C>T

Variant summary

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

The ENST00000443237.2(ENSG00000228033):​n.185-15073C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,936 control chromosomes in the GnomAD database, including 26,432 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 (26432 hom., cov: 32)
• Consequence: ENSG00000228033 ENST00000443237.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443237.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369165	NR_187747.1		n.172-15073C>T		intron	N/A
	LOC105369165	NR_187748.1		n.253-9114C>T		intron	N/A
	LOC105369165	NR_187749.1		n.221-15073C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228033	ENST00000421575.7	TSL:5	n.240-9114C>T		intron	N/A
	ENSG00000228033	ENST00000443237.2	TSL:3	n.185-15073C>T		intron	N/A
	ENSG00000228033	ENST00000668945.1		n.220-15073C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88946 AN: 151816 Hom.: 26417 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.586 AC: 89001 AN: 151936 Hom.: 26432 Cov.: 32 AF XY: 0.582 AC XY: 43180 AN XY: 74246

African (AFR) AF: 0.598 AC: 24765 AN: 41428

American (AMR) AF: 0.583 AC: 8906 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2060 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2276 AN: 5164

South Asian (SAS) AF: 0.513 AC: 2456 AN: 4792

European-Finnish (FIN) AF: 0.534 AC: 5648 AN: 10568

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40630 AN: 67936

Other (OTH) AF: 0.630 AC: 1329 AN: 2108

Alfa AF: 0.590 Hom.: 14523

Bravo AF: 0.590

Asia WGS AF: 0.479 AC: 1668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.7
DANN	Benign	0.23
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1319797; hg19: chr2-52969029;