rs360719

Positions:

• chr11-112165426-A-G

Variant summary

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

The ENST00000527589.1(ENSG00000254638):​n.365T>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 0.252 in 152,150 control chromosomes in the GnomAD database, including 5,024 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 0.25 (5024 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENST00000527589.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987164	XR_001748384.2	n.276T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000527589.1	n.365T>C		non_coding_transcript_exon_variant	4/4	3

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38321 AN: 152030 Hom.: 5025 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.252 AC: 38313 AN: 152148 Hom.: 5024 Cov.: 33 AF XY: 0.252 AC XY: 18757 AN XY: 74388

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.248

Alfa AF: 0.252 Hom.: 681

Bravo AF: 0.253

Asia WGS AF: 0.186 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs360719; hg19: chr11-112036149;