14-44870240-T-C

Variant names:

• chr14-44870240-T-C
• rs17115674

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 0.0778 in 152,232 control chromosomes in the GnomAD database, including 615 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 0.078 (615 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 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: 0.0778 AC: 11838 AN: 152114 Hom.: 615 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0549

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0399

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0778 AC: 11849 AN: 152232 Hom.: 615 Cov.: 31 AF XY: 0.0799 AC XY: 5947 AN XY: 74430

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0824

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0399

Gnomad4 OTH AF: 0.0718

Alfa AF: 0.0561 Hom.: 95

Bravo AF: 0.0794

Asia WGS AF: 0.0950 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17115674; hg19: chr14-45339443;