chr14-56005769-C-T

Variant names:

• chr14-56005769-C-T
• rs922656
• XR_007064183.1:n.1082C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064183.1(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_007064183.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 3 publications found

Genes affected

LOC105370512 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.227 AC: 9423 AN: 41470

American (AMR) AF: 0.484 AC: 7404 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3005 AN: 5156

South Asian (SAS) AF: 0.399 AC: 1920 AN: 4818

European-Finnish (FIN) AF: 0.481 AC: 5085 AN: 10580

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36822 AN: 67942

Other (OTH) AF: 0.489 AC: 1035 AN: 2116

Alfa AF: 0.511 Hom.: 34742

Bravo AF: 0.439

Asia WGS AF: 0.433 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs922656; hg19: chr14-56472487;