rs1426391

chr11-116072535-A-C

Variant summary

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

The XR_948056.2(LOC105369513):n.314-5330T>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 0.389 in 151,686 control chromosomes in the GnomAD database, including 12,805 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 0.39 (12805 hom., cov: 30)
• Consequence: LOC105369513 XR_948056.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

LOC105369513 (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 (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369513	XR_948056.2	n.314-5330T>G		intron_variant, non_coding_transcript_variant
LOC105369513	XR_001748401.1	n.192+479T>G		intron_variant, non_coding_transcript_variant
LOC105369513	XR_948055.2	n.192+479T>G		intron_variant, non_coding_transcript_variant
LOC105369513	XR_948057.2	n.97+574T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59025 AN: 151570 Hom.: 12797 Cov.: 30

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.389 AC: 59050 AN: 151686 Hom.: 12805 Cov.: 30 AF XY: 0.386 AC XY: 28601 AN XY: 74082

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.402

Alfa AF: 0.470 Hom.: 19852

Bravo AF: 0.373

Asia WGS AF: 0.371 AC: 1293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.33
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1426391; hg19: chr11-115943253;