14-56005769-C-T

Position:

• chr14-56005769-C-T

Variant summary

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

The XR_943899.3(LOC105370512):​n.1082C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,040 control chromosomes in the GnomAD database, including 16,224 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 0.44 (16224 hom., cov: 32)
• Consequence: LOC105370512 XR_943899.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

LOC105370512 (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 (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370512	XR_007064183.1	n.1082C>T		non_coding_transcript_exon_variant	1/4
LOC105370512	XR_943899.3	n.1082C>T		non_coding_transcript_exon_variant	1/3
		n.56005769C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67030 AN: 151922 Hom.: 16227 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.441 AC: 67032 AN: 152040 Hom.: 16224 Cov.: 32 AF XY: 0.439 AC XY: 32631 AN XY: 74322

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.489

Alfa AF: 0.519 Hom.: 28218

Bravo AF: 0.439

Asia WGS AF: 0.433 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs922656; hg19: chr14-56472487;