rs10144042

Positions:

• chr14-98033121-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.287

Alfa AF: 0.250 Hom.: 4932

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10144042; hg19: chr14-98499458;