14-42719707-C-T

Variant names:

• chr14-42719707-C-T
• rs1777077

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.738 in 151,922 control chromosomes in the GnomAD database, including 41,786 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 0.74 (41786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.738 AC: 111966 AN: 151804 Hom.: 41751 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.738 AC: 112057 AN: 151922 Hom.: 41786 Cov.: 31 AF XY: 0.738 AC XY: 54774 AN XY: 74218

African (AFR) AF: 0.708 AC: 29346 AN: 41452

American (AMR) AF: 0.726 AC: 11059 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2746 AN: 5130

South Asian (SAS) AF: 0.655 AC: 3154 AN: 4814

European-Finnish (FIN) AF: 0.836 AC: 8820 AN: 10546

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52160 AN: 67968

Other (OTH) AF: 0.721 AC: 1519 AN: 2106

Alfa AF: 0.751 Hom.: 44088

Bravo AF: 0.725

Asia WGS AF: 0.654 AC: 2277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	18
DANN	Benign	0.69
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1777077; hg19: chr14-43188910;