chr14-77260390-C-T

Variant names:

• chr14-77260390-C-T
• rs888060
• XR_007064276.1:n.572C>T

Variant summary

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

The XR_007064276.1(LOC124903351):​n.572C>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 0.107 in 152,260 control chromosomes in the GnomAD database, including 1,117 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 0.11 (1117 hom., cov: 33)
• Consequence: LOC124903351 XR_007064276.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 5 publications found

Genes affected

LOC124903351 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16243 AN: 152142 Hom.: 1116 Cov.: 33

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00885

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.107 AC: 16244 AN: 152260 Hom.: 1117 Cov.: 33 AF XY: 0.108 AC XY: 8022 AN XY: 74434

African (AFR) AF: 0.0366 AC: 1522 AN: 41574

American (AMR) AF: 0.0792 AC: 1212 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3468

East Asian (EAS) AF: 0.00887 AC: 46 AN: 5184

South Asian (SAS) AF: 0.183 AC: 883 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1423 AN: 10590

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10230 AN: 68004

Other (OTH) AF: 0.0999 AC: 211 AN: 2112

Alfa AF: 0.138 Hom.: 1368

Bravo AF: 0.0959

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.82
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs888060; hg19: chr14-77726733;