rs10129426

Variant names:

• chr14-103552118-G-A
• rs10129426
• XR_007064357.1:n.1364C>T

Variant summary

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

The XR_007064357.1(LOC124903392):​n.1364C>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 0.537 in 152,164 control chromosomes in the GnomAD database, including 21,989 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 0.54 (21989 hom., cov: 34)
• Consequence: LOC124903392 XR_007064357.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 14 publications found

Genes affected

LOC124903392 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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: 0.537 AC: 81574 AN: 152046 Hom.: 21968 Cov.: 34

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.537 AC: 81647 AN: 152164 Hom.: 21989 Cov.: 34 AF XY: 0.533 AC XY: 39658 AN XY: 74366

African (AFR) AF: 0.574 AC: 23848 AN: 41532

American (AMR) AF: 0.480 AC: 7346 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2326 AN: 5170

South Asian (SAS) AF: 0.398 AC: 1923 AN: 4828

European-Finnish (FIN) AF: 0.569 AC: 6021 AN: 10586

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36466 AN: 67970

Other (OTH) AF: 0.529 AC: 1116 AN: 2110

Alfa AF: 0.537 Hom.: 68000

Bravo AF: 0.536

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.37
PhyloP100		-0.74

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10129426;

hg19: chr14-104018455;