rs10144042

Variant names:

• chr14-98033121-G-A
• rs10144042
• XR_001750874.2:n.*131C>T

Variant summary

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

The XR_001750874.2(LOC107984706):​n.*131C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,924 control chromosomes in the GnomAD database, including 5,110 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 0.25 (5110 hom., cov: 32)
• Consequence: LOC107984706 XR_001750874.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 5 publications found

Genes affected

LOC107984706 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984706	XR_001750874.2	n.*131C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38666 AN: 151804 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.255 AC: 38708 AN: 151924 Hom.: 5110 Cov.: 32 AF XY: 0.258 AC XY: 19178 AN XY: 74264

African (AFR) AF: 0.234 AC: 9707 AN: 41418

American (AMR) AF: 0.339 AC: 5174 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1805 AN: 5132

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4818

European-Finnish (FIN) AF: 0.271 AC: 2864 AN: 10552

Middle Eastern (MID) AF: 0.315 AC: 92 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16211 AN: 67954

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.247 Hom.: 12632

Bravo AF: 0.260

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10144042; hg19: chr14-98499458; COSMIC: COSV107181253;