14-42029870-T-C

Variant names:

• chr14-42029870-T-C
• rs1684720

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 0.595 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.727 AC: 30088 AN: 41380

American (AMR) AF: 0.633 AC: 9659 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1909 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3569 AN: 5126

South Asian (SAS) AF: 0.571 AC: 2754 AN: 4820

European-Finnish (FIN) AF: 0.425 AC: 4477 AN: 10526

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35916 AN: 67834

Other (OTH) AF: 0.575 AC: 1214 AN: 2110

Alfa AF: 0.574 Hom.: 3223

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs1684720; hg19: chr14-42499073;