rs4904868

Positions:

• chr14-92314657-T-C

Variant summary

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

The XR_944153.1(LOC105370627):​n.132-589T>C 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 0.426 in 152,142 control chromosomes in the GnomAD database, including 15,493 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 0.43 (15493 hom., cov: 33)
• Consequence: LOC105370627 XR_944153.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

LOC105370627 (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 (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370627	XR_944153.1	n.132-589T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64860 AN: 152024 Hom.: 15488 Cov.: 33

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.426 AC: 64883 AN: 152142 Hom.: 15493 Cov.: 33 AF XY: 0.423 AC XY: 31491 AN XY: 74368

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.415

Alfa AF: 0.516 Hom.: 41563

Bravo AF: 0.399

Asia WGS AF: 0.387 AC: 1345 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	0.43
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4904868; hg19: chr14-92781001;