11-116446060-T-C

Variant summary

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

The XR_001748403.2(LOC107987166):n.349+27817A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,984 control chromosomes in the GnomAD database, including 13,512 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 0.41 (13512 hom., cov: 31)
• Consequence: LOC107987166 XR_001748403.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

LOC107987166 (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 (AMR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987166	XR_001748403.2	n.349+27817A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62919 AN: 151866 Hom.: 13517 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.412

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.414 AC: 62926 AN: 151984 Hom.: 13512 Cov.: 31 AF XY: 0.418 AC XY: 31072 AN XY: 74284

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.410

Alfa AF: 0.443 Hom.: 19825

Bravo AF: 0.411

Asia WGS AF: 0.311 AC: 1084 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	9.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs489164; hg19: chr11-116316777;