rs10142119

Variant names:

• chr14-98020208-G-A
• rs10142119

Your query was ambiguous. Multiple possible variants found:

• chr14-98020208-G-A
• chr14-98020208-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.402 AC: 16653 AN: 41448

American (AMR) AF: 0.647 AC: 9887 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2364 AN: 3468

East Asian (EAS) AF: 0.390 AC: 2012 AN: 5154

South Asian (SAS) AF: 0.449 AC: 2163 AN: 4818

European-Finnish (FIN) AF: 0.587 AC: 6197 AN: 10558

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.717 AC: 48738 AN: 67978

Other (OTH) AF: 0.604 AC: 1278 AN: 2116

Alfa AF: 0.676 Hom.: 112304

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
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs10142119; hg19: chr14-98486545;