19-44370295-G-C

Position:

• chr19-44370295-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000267173 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44370295G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267173	ENST00000588212.1	c.15+26904C>G		intron_variant		2		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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.429

Alfa AF: 0.432 Hom.: 1994

Bravo AF: 0.377

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2722750; hg19: chr19-44874455;