14-42885658-C-T

Variant names:

• chr14-42885658-C-T
• rs17113620

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 0.0405 in 151,798 control chromosomes in the GnomAD database, including 174 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 0.040 (174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0405 AC: 6142 AN: 151682 Hom.: 175 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0309

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

GnomAD4 genome AF: 0.0405 AC: 6141 AN: 151798 Hom.: 174 Cov.: 32 AF XY: 0.0414 AC XY: 3069 AN XY: 74140

African (AFR) AF: 0.0320 AC: 1328 AN: 41478

American (AMR) AF: 0.0327 AC: 497 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3470

East Asian (EAS) AF: 0.137 AC: 705 AN: 5156

South Asian (SAS) AF: 0.0530 AC: 255 AN: 4812

European-Finnish (FIN) AF: 0.0480 AC: 507 AN: 10572

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0403 AC: 2732 AN: 67824

Other (OTH) AF: 0.0306 AC: 64 AN: 2090

Alfa AF: 0.0378 Hom.: 140

Bravo AF: 0.0395

Asia WGS AF: 0.0680 AC: 236 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.31
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs17113620; hg19: chr14-43354861;