chr14-24341692-C-T

Variant names:

• chr14-24341692-C-T
• rs3212240

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 0.431 in 152,108 control chromosomes in the GnomAD database, including 16,649 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 0.43 (16649 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 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: 0.431 AC: 65575 AN: 151990 Hom.: 16649 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.431 AC: 65587 AN: 152108 Hom.: 16649 Cov.: 32 AF XY: 0.429 AC XY: 31898 AN XY: 74372

African (AFR) AF: 0.183 AC: 7608 AN: 41502

American (AMR) AF: 0.429 AC: 6546 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2161 AN: 3464

East Asian (EAS) AF: 0.155 AC: 803 AN: 5180

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4820

European-Finnish (FIN) AF: 0.582 AC: 6156 AN: 10574

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38924 AN: 67994

Other (OTH) AF: 0.450 AC: 951 AN: 2112

Alfa AF: 0.515 Hom.: 10163

Bravo AF: 0.408

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.33
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3212240; hg19: chr14-24810898;