ENST00000588212.1:c.15+26904C>G

Variant names:

• chr19-44370295-G-C
• rs2722750
• ENST00000588212.1:c.15+26904C>G

Variant summary

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

The ENST00000588212.1(ENSG00000267173):​c.15+26904C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,050 control chromosomes in the GnomAD database, including 13,969 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 0.39 (13969 hom., cov: 32)
• Consequence: ENSG00000267173 ENST00000588212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 2 publications found

Genes affected

ENSG00000267173 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000588212.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267173	ENST00000588212.1	TSL:2	c.15+26904C>G		intron	N/A	ENSP00000468271.1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59255 AN: 151932 Hom.: 13971 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.390 AC: 59248 AN: 152050 Hom.: 13969 Cov.: 32 AF XY: 0.392 AC XY: 29102 AN XY: 74304

African (AFR) AF: 0.108 AC: 4469 AN: 41502

American (AMR) AF: 0.446 AC: 6815 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1792 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2914 AN: 5170

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4818

European-Finnish (FIN) AF: 0.438 AC: 4624 AN: 10552

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34454 AN: 67940

Other (OTH) AF: 0.429 AC: 907 AN: 2112

Alfa AF: 0.432 Hom.: 1994

Bravo AF: 0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2722750; hg19: chr19-44874455;