14-44638258-C-G

Variant names:

• chr14-44638258-C-G
• rs2415872

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 0.55 in 148,022 control chromosomes in the GnomAD database, including 22,938 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 0.55 (22938 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 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: 0.550 AC: 81293 AN: 147904 Hom.: 22900 Cov.: 24

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.550 AC: 81381 AN: 148022 Hom.: 22938 Cov.: 24 AF XY: 0.548 AC XY: 39438 AN XY: 71974

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.549

Alfa AF: 0.373 Hom.: 916

Bravo AF: 0.561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2415872; hg19: chr14-45107461; COSMIC: COSV53414563;