14-24511286-A-G

Variant names:

• chr14-24511286-A-G
• rs1956917

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 0.554 in 152,024 control chromosomes in the GnomAD database, including 24,356 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 (24356 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.554 AC: 84216 AN: 151906 Hom.: 24347 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.554 AC: 84262 AN: 152024 Hom.: 24356 Cov.: 31 AF XY: 0.547 AC XY: 40644 AN XY: 74300

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.540

Alfa AF: 0.595 Hom.: 21165

Bravo AF: 0.532

Asia WGS AF: 0.365 AC: 1270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1956917; hg19: chr14-24980492;