rs10142119

chr14-98020208-G-Achr14-98020208-G-C

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 0.594 in 152,022 control chromosomes in the GnomAD database, including 28,389 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 0.59 (28389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 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: 0.594 AC: 90211 AN: 151902 Hom.: 28390 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.824

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.594 AC: 90237 AN: 152022 Hom.: 28389 Cov.: 32 AF XY: 0.584 AC XY: 43364 AN XY: 74314

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.604

Alfa AF: 0.694 Hom.: 73874

Bravo AF: 0.595

Asia WGS AF: 0.407 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.98
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10142119; hg19: chr14-98486545;