14-46599121-T-G

Position:

• chr14-46599121-T-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 0.615 in 151,666 control chromosomes in the GnomAD database, including 28,929 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 0.62 (28929 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46599121T>G		intergenic_region
LOC105370481	XR_001750753.1	n.814-1632A>C		intron_variant
LOC105370481	XR_001750754.1	n.674-1632A>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93256 AN: 151548 Hom.: 28903 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.615 AC: 93330 AN: 151666 Hom.: 28929 Cov.: 32 AF XY: 0.619 AC XY: 45870 AN XY: 74128

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.597

Alfa AF: 0.598 Hom.: 14003

Bravo AF: 0.608

Asia WGS AF: 0.587 AC: 2036 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472242; hg19: chr14-47068324;