19-53788035-C-T

Position:

• chr19-53788035-C-T

Variant summary

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

The ENST00000595160.1(ENSG00000269877):​n.135G>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 0.116 in 389,630 control chromosomes in the GnomAD database, including 2,979 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 (1520 hom., cov: 31)
  • Exomes 𝑓: 0.11 (1459 hom.)
• Consequence: ENSG00000269877 ENST00000595160.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

ENSG00000269877 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904767	XR_007067336.1	n.191G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000269877	ENST00000595160.1	n.135G>A		non_coding_transcript_exon_variant	1/2	3
ENSG00000269564	ENST00000597420.2	n.90-562C>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20260 AN: 151820 Hom.: 1512 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.105 AC: 24998 AN: 237692 Hom.: 1459 Cov.: 0 AF XY: 0.103 AC XY: 13476 AN XY: 130698

Gnomad4 AFR exome AF: 0.187

Gnomad4 AMR exome AF: 0.110

Gnomad4 ASJ exome AF: 0.0814

Gnomad4 EAS exome AF: 0.134

Gnomad4 SAS exome AF: 0.0891

Gnomad4 FIN exome AF: 0.0797

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.134 AC: 20294 AN: 151938 Hom.: 1520 Cov.: 31 AF XY: 0.131 AC XY: 9710 AN XY: 74274

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0747

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.0969

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.143

Alfa AF: 0.120 Hom.: 247

Bravo AF: 0.141

Asia WGS AF: 0.152 AC: 528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28461391; hg19: chr19-54291289;