rs10484035

Positions:

• chr14-92312213-C-T

Variant summary

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

The XR_944153.1(LOC105370627):​n.132-3033C>T 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 0.45 in 151,878 control chromosomes in the GnomAD database, including 16,146 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 0.45 (16146 hom., cov: 31)
• Consequence: LOC105370627 XR_944153.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

LOC105370627 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370627	XR_944153.1	n.132-3033C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68271 AN: 151760 Hom.: 16109 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.450 AC: 68360 AN: 151878 Hom.: 16146 Cov.: 31 AF XY: 0.457 AC XY: 33948 AN XY: 74220

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.482

Alfa AF: 0.423 Hom.: 3742

Bravo AF: 0.467

Asia WGS AF: 0.551 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484035; hg19: chr14-92778557;