rs2184283

Positions:

• chr14-20438455-G-C
• chr14-20438455-G-T

Variant summary

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

The ENST00000553568.1(ENSG00000259162):​n.75-51G>C 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 0.386 in 151,950 control chromosomes in the GnomAD database, including 12,034 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 0.39 (12032 hom., cov: 31)
  • Exomes 𝑓: 0.32 (2 hom.)
• Consequence: ENST00000553568.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000553568.1	n.75-51G>C		intron_variant, non_coding_transcript_variant
	ENST00000700970.1	n.337+418G>C		intron_variant, non_coding_transcript_variant
	ENST00000687238.1	n.338-198G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58568 AN: 151798 Hom.: 12015 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.324 AC: 11 AN: 34 Hom.: 2 Cov.: 0 AF XY: 0.150 AC XY: 3 AN XY: 20

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.386 AC: 58629 AN: 151916 Hom.: 12032 Cov.: 31 AF XY: 0.386 AC XY: 28654 AN XY: 74260

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.369

Alfa AF: 0.188 Hom.: 326

Bravo AF: 0.399

Asia WGS AF: 0.323 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2184283; hg19: chr14-20906614;