chr14-57355498-G-A

Position:

• chr14-57355498-G-A

Variant summary

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

The ENST00000556602.1(ENSG00000259008):​n.53G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 152,062 control chromosomes in the GnomAD database, including 32,434 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 0.60 (32433 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENSG00000259008 ENST00000556602.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

ENSG00000259008 (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 = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57355498G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259008	ENST00000556602.1	n.53G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91625 AN: 151942 Hom.: 32449 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.602 AC: 91607 AN: 152060 Hom.: 32433 Cov.: 32 AF XY: 0.607 AC XY: 45127 AN XY: 74326

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.632

Alfa AF: 0.731 Hom.: 56782

Bravo AF: 0.574

Asia WGS AF: 0.628 AC: 2188 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	6.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7144649; hg19: chr14-57822216;