rs1981266

Variant names:

• chr14-101213181-C-T
• rs1981266

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.238 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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0364

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.257

Alfa AF: 0.238 Hom.: 1628

Bravo AF: 0.246

Asia WGS AF: 0.0980 AC: 340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981266; hg19: chr14-101679518;