rs2023414

chr19-19749686-C-T

Variant summary

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

The XR_007067367.1(LOC101060187):n.2403G>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 0.209 in 152,220 control chromosomes in the GnomAD database, including 3,835 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 0.21 (3832 hom., cov: 33)
  • Exomes 𝑓: 0.26 (3 hom.)
• Consequence: LOC101060187 XR_007067367.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

LOC101060187 (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 = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101060187	XR_007067367.1	n.2403G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000617163.1	n.1050-51C>T		intron_variant, non_coding_transcript_variant
	ENST00000651161.1	n.2218G>A		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31820 AN: 151990 Hom.: 3832 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.216

GnomAD4 exome AF: 0.259 AC: 29 AN: 112 Hom.: 3 AF XY: 0.231 AC XY: 18 AN XY: 78

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.429

Gnomad4 NFE exome AF: 0.233

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.209 AC: 31823 AN: 152108 Hom.: 3832 Cov.: 33 AF XY: 0.211 AC XY: 15717 AN XY: 74348

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.214

Alfa AF: 0.250 Hom.: 7991

Bravo AF: 0.203

Asia WGS AF: 0.135 AC: 472 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	4.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2023414; hg19: chr19-19860495;