14-73469892-C-T

Position:

• chr14-73469892-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515412.3(ENSG00000251393):​n.516+6156C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 151,782 control chromosomes in the GnomAD database, including 49,349 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 0.80 (49349 hom., cov: 29)
• Consequence: ENST00000515412.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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
	ENST00000515412.3	n.516+6156C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121359 AN: 151666 Hom.: 49291 Cov.: 29

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.800 AC: 121468 AN: 151782 Hom.: 49349 Cov.: 29 AF XY: 0.804 AC XY: 59610 AN XY: 74124

Gnomad4 AFR AF: 0.950

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.795

Alfa AF: 0.741 Hom.: 20980

Bravo AF: 0.811

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4899468; hg19: chr14-73936597;