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.

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: 0.255 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 v4.9

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;