14-92309818-A-C

Position:

• chr14-92309818-A-C

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 0.427 in 151,968 control chromosomes in the GnomAD database, including 15,483 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 0.43 (15483 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.92309818A>C		intergenic_region
LOC105370627	XR_944153.1	n.131+5274A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64894 AN: 151850 Hom.: 15477 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.427 AC: 64918 AN: 151968 Hom.: 15483 Cov.: 31 AF XY: 0.424 AC XY: 31497 AN XY: 74286

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.415

Alfa AF: 0.464 Hom.: 2968

Bravo AF: 0.400

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.11
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075830; hg19: chr14-92776162;