rs10139381

chr14-46613802-T-C

Variant summary

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

The XR_001750753.1(LOC105370481):n.813+1315A>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 0.232 in 151,514 control chromosomes in the GnomAD database, including 4,351 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 0.23 (4351 hom., cov: 32)
• Consequence: LOC105370481 XR_001750753.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

LOC105370481 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370481	XR_001750753.1	n.813+1315A>G		intron_variant, non_coding_transcript_variant
LOC105370481	XR_001750754.1	n.673+1315A>G		intron_variant, non_coding_transcript_variant
LOC105370481	XR_001750755.1	n.717+1315A>G		intron_variant, non_coding_transcript_variant
LOC105370481	XR_943828.2	n.813+1315A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35219 AN: 151396 Hom.: 4355 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.0823

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.232 AC: 35214 AN: 151514 Hom.: 4351 Cov.: 32 AF XY: 0.228 AC XY: 16904 AN XY: 74062

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.0815

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.243

Alfa AF: 0.253 Hom.: 2342

Bravo AF: 0.233

Asia WGS AF: 0.159 AC: 545 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	10
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: rs10139381; hg19: chr14-47083005;