chr19-44910109-T-C

Position:

• chr19-44910109-T-C

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.735T>C 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 0.0705 in 152,124 control chromosomes in the GnomAD database, including 630 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 0.071 (630 hom., cov: 31)
  • Exomes 𝑓: 0.038 (0 hom.)
• Consequence: ENSG00000280087 ENST00000623895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.44910109T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000280087	ENST00000623895.1	n.735T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10721 AN: 151980 Hom.: 630 Cov.: 31

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0598

Gnomad ASJ AF: 0.0875

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0736

GnomAD4 exome AF: 0.0385 AC: 1 AN: 26 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.0455

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0705 AC: 10727 AN: 152098 Hom.: 630 Cov.: 31 AF XY: 0.0754 AC XY: 5607 AN XY: 74356

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.0598

Gnomad4 ASJ AF: 0.0875

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0407

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.0900

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0765 Hom.: 76

Bravo AF: 0.0569

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1081106; hg19: chr19-45413366;