chr14-50857024-G-A

Position:

• chr14-50857024-G-A

Variant summary

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

The ENST00000557152.1(ENSG00000258687):​n.29-8490G>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 0.375 in 152,012 control chromosomes in the GnomAD database, including 11,341 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 0.38 (11341 hom., cov: 31)
• Consequence: ENST00000557152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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
	ENST00000557152.1	n.29-8490G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56917 AN: 151894 Hom.: 11310 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.375 AC: 57007 AN: 152012 Hom.: 11341 Cov.: 31 AF XY: 0.376 AC XY: 27911 AN XY: 74308

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.382

Alfa AF: 0.325 Hom.: 5425

Bravo AF: 0.400

Asia WGS AF: 0.391 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8019546; hg19: chr14-51323742;