14-42029870-T-C

Variant names:

• chr14-42029870-T-C
• rs1684720

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;