chr14-101213181-C-T

Variant names:

• chr14-101213181-C-T
• rs1981266

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 0.238 in 152,032 control chromosomes in the GnomAD database, including 4,603 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 0.24 (4603 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.238 AC: 36188 AN: 151914 Hom.: 4595 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.238 AC: 36233 AN: 152032 Hom.: 4603 Cov.: 33 AF XY: 0.232 AC XY: 17272 AN XY: 74310

African (AFR) AF: 0.298 AC: 12329 AN: 41420

American (AMR) AF: 0.242 AC: 3702 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3468

East Asian (EAS) AF: 0.0364 AC: 188 AN: 5168

South Asian (SAS) AF: 0.123 AC: 594 AN: 4824

European-Finnish (FIN) AF: 0.184 AC: 1950 AN: 10572

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16011 AN: 67972

Other (OTH) AF: 0.257 AC: 543 AN: 2112

Alfa AF: 0.234 Hom.: 2662

Bravo AF: 0.246

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.63
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1981266; hg19: chr14-101679518;