14-42029870-T-C

Position:

• chr14-42029870-T-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 0.595 in 151,724 control chromosomes in the GnomAD database, including 27,562 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 0.60 (27562 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.42029870T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90204 AN: 151604 Hom.: 27509 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.595 AC: 90319 AN: 151724 Hom.: 27562 Cov.: 33 AF XY: 0.590 AC XY: 43774 AN XY: 74138

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.575

Alfa AF: 0.567 Hom.: 3010

Bravo AF: 0.619

Asia WGS AF: 0.623 AC: 2164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1684720; hg19: chr14-42499073;