14-56722189-C-T

Variant summary

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

The ENST00000554597.5(ENSG00000259133):n.369+3701G>A 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 0.848 in 152,142 control chromosomes in the GnomAD database, including 55,569 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 0.85 (55569 hom., cov: 32)
• Consequence: ENST00000554597.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554597.5	n.369+3701G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128990 AN: 152024 Hom.: 55559 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.936

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.848 AC: 129034 AN: 152142 Hom.: 55569 Cov.: 32 AF XY: 0.847 AC XY: 62994 AN XY: 74384

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.936

Gnomad4 OTH AF: 0.866

Alfa AF: 0.921 Hom.: 90373

Bravo AF: 0.830

Asia WGS AF: 0.809 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.3
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs198247; hg19: chr14-57188907; COSMIC: COSV73551727;