11-116362926-A-T

Variant summary

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

The XR_001748403.2(LOC107987166):n.350-42487T>A 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 0.402 in 152,088 control chromosomes in the GnomAD database, including 12,931 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 0.40 (12931 hom., cov: 33)
• Consequence: LOC107987166 XR_001748403.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

Genes affected

LOC107987166 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987166	XR_001748403.2	n.350-42487T>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61124 AN: 151970 Hom.: 12904 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.402 AC: 61209 AN: 152088 Hom.: 12931 Cov.: 33 AF XY: 0.402 AC XY: 29910 AN XY: 74346

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.385

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.398

Alfa AF: 0.220 Hom.: 464

Bravo AF: 0.395

Asia WGS AF: 0.425 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	12
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs572619; hg19: chr11-116233643;