19-44909976-G-T

Position:

• chr19-44909976-G-T

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.602G>T 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 0.0809 in 151,942 control chromosomes in the GnomAD database, including 631 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 0.081 (629 hom., cov: 31)
  • Exomes 𝑓: 0.042 (2 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280087	ENST00000623895.1	n.602G>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12261 AN: 151288 Hom.: 629 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0698

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.0367

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.0812

GnomAD4 exome AF: 0.0424 AC: 23 AN: 542 Hom.: 2 Cov.: 0 AF XY: 0.0395 AC XY: 14 AN XY: 354

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR 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: 0.0505

Gnomad4 OTH exome AF: 0.0417

GnomAD4 genome AF: 0.0810 AC: 12269 AN: 151400 Hom.: 629 Cov.: 31 AF XY: 0.0773 AC XY: 5718 AN XY: 73982

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0698

Gnomad4 EAS AF: 0.0811

Gnomad4 SAS AF: 0.0371

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0797

Gnomad4 OTH AF: 0.0823

Alfa AF: 0.0372 Hom.: 34

Bravo AF: 0.0814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1065853; hg19: chr19-45413233;