14-92935748-C-G

Position:

• chr14-92935748-C-G

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 0.589 in 152,124 control chromosomes in the GnomAD database, including 26,841 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 0.59 (26841 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89595 AN: 152006 Hom.: 26831 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.589 AC: 89642 AN: 152124 Hom.: 26841 Cov.: 33 AF XY: 0.590 AC XY: 43892 AN XY: 74386

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.708

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.607

Alfa AF: 0.422 Hom.: 1068

Bravo AF: 0.585

Asia WGS AF: 0.715 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.27
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs875395; hg19: chr14-93402093;