chr14-103552118-G-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903392	XR_007064357.1	n.1364C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

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 v4.3

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

Other links and lift over

dbSNP: rs10129426; hg19: chr14-104018455;