14-68871717-C-T

Variant names:

• chr14-68871717-C-T
• rs4312253

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 0.69 in 152,028 control chromosomes in the GnomAD database, including 36,371 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 0.69 (36371 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.285

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.756 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: 0.690 AC: 104849 AN: 151910 Hom.: 36341 Cov.: 31

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.690 AC: 104923 AN: 152028 Hom.: 36371 Cov.: 31 AF XY: 0.691 AC XY: 51345 AN XY: 74326

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.694

Alfa AF: 0.685 Hom.: 4453

Bravo AF: 0.695

Asia WGS AF: 0.701 AC: 2434 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4312253; hg19: chr14-69338434;