19-49720009-G-A

Position:

• chr19-49720009-G-A

Variant summary

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

The ENST00000498085.1(ENSG00000243829):​n.73C>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 0.0209 in 1,611,544 control chromosomes in the GnomAD database, including 2,625 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 0.060 (677 hom., cov: 31)
  • Exomes 𝑓: 0.017 (1948 hom.)
• Consequence: ENST00000498085.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 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
	ENST00000498085.1	n.73C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9048 AN: 151904 Hom.: 673 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.00312

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00176

Gnomad OTH AF: 0.0527

GnomAD4 exome AF: 0.0169 AC: 24627 AN: 1459524 Hom.: 1948 Cov.: 33 AF XY: 0.0158 AC XY: 11494 AN XY: 726084

Gnomad4 AFR exome AF: 0.157

Gnomad4 AMR exome AF: 0.174

Gnomad4 ASJ exome AF: 0.00394

Gnomad4 EAS exome AF: 0.178

Gnomad4 SAS exome AF: 0.0194

Gnomad4 FIN exome AF: 0.00307

Gnomad4 NFE exome AF: 0.000980

Gnomad4 OTH exome AF: 0.0246

GnomAD4 genome AF: 0.0597 AC: 9069 AN: 152020 Hom.: 677 Cov.: 31 AF XY: 0.0599 AC XY: 4451 AN XY: 74310

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.0256

Gnomad4 FIN AF: 0.00312

Gnomad4 NFE AF: 0.00176

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.00678 Hom.: 20

Bravo AF: 0.0749

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.3
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3810265; hg19: chr19-50223266;