11-112960736-A-G

Variant summary

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

The NR_120563.1(LOC101928847):n.477T>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 0.0875 in 152,238 control chromosomes in the GnomAD database, including 1,198 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 0.087 (1198 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC101928847 NR_120563.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928847	NR_120563.1	n.477T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000500537.2	n.477T>C		non_coding_transcript_exon_variant	3/3	1

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13285 AN: 152120 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00479

Gnomad OTH AF: 0.0665

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0875 AC: 13314 AN: 152238 Hom.: 1198 Cov.: 32 AF XY: 0.0948 AC XY: 7053 AN XY: 74430

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.00891

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.00479

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0175 Hom.: 252

Bravo AF: 0.0929

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.4
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2301228; hg19: chr11-112831459;