chr19-44912456-G-A

Position:

• chr19-44912456-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000623895.1(ENSG00000280087):​n.3082G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,240 control chromosomes in the GnomAD database, including 1,479 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 0.13 (1479 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44912456G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280087	ENST00000623895.1	n.3082G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20281 AN: 152012 Hom.: 1469 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0978

GnomAD4 exome AF: 0.100 AC: 11 AN: 110 Hom.: 0 Cov.: 0 AF XY: 0.0921 AC XY: 7 AN XY: 76

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.134 AC: 20323 AN: 152130 Hom.: 1479 Cov.: 32 AF XY: 0.136 AC XY: 10114 AN XY: 74356

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0939

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.0967

Gnomad4 SAS AF: 0.0769

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.102

Alfa AF: 0.123 Hom.: 144

Bravo AF: 0.130

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10414043; hg19: chr19-45415713;