14-82788861-G-C

Position:

• chr14-82788861-G-C

Variant summary

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

The ENST00000554451.1(ENSG00000258683):​n.156C>G 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 0.0882 in 152,230 control chromosomes in the GnomAD database, including 954 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 0.088 (952 hom., cov: 32)
  • Exomes 𝑓: 0.30 (2 hom.)
• Consequence: ENST00000554451.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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
	ENST00000554451.1	n.156C>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13411 AN: 152092 Hom.: 945 Cov.: 32

Gnomad AFR AF: 0.0232

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.300 AC: 6 AN: 20 Hom.: 2 Cov.: 0 AF XY: 0.375 AC XY: 6 AN XY: 16

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0882 AC: 13424 AN: 152210 Hom.: 952 Cov.: 32 AF XY: 0.0938 AC XY: 6983 AN XY: 74412

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0417 Hom.: 30

Bravo AF: 0.0936

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs746630; hg19: chr14-83255205;