14-73469892-C-T

Variant names:

• chr14-73469892-C-T
• rs4899468
• ENST00000515412.3:n.516+6156C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515412.3(ENSG00000251393):​n.516+6156C>T variant causes a intron 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: ENSG00000251393 ENST00000515412.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 5 publications found

Genes affected

ENSG00000251393 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515412.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251393	ENST00000515412.3	TSL:5	n.516+6156C>T		intron	N/A

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

African (AFR) AF: 0.950 AC: 39342 AN: 41416

American (AMR) AF: 0.800 AC: 12147 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2648 AN: 3466

East Asian (EAS) AF: 0.866 AC: 4485 AN: 5180

South Asian (SAS) AF: 0.770 AC: 3707 AN: 4812

European-Finnish (FIN) AF: 0.783 AC: 8187 AN: 10450

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48449 AN: 67962

Other (OTH) AF: 0.795 AC: 1669 AN: 2100

Alfa AF: 0.739 Hom.: 23026

Bravo AF: 0.811

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4899468; hg19: chr14-73936597;