rs10129426

Positions:

• chr14-103552118-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903392 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903392	XR_007064357.1	n.1364C>T		non_coding_transcript_exon_variant	1/2

Ensembl

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

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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.529

Alfa AF: 0.534 Hom.: 23067

Bravo AF: 0.536

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10129426; hg19: chr14-104018455;