rs4905110

Positions:

• chr14-93895984-G-A
• chr14-93895984-G-T

Variant summary

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

The ENST00000623423.1(ENSG00000279593):​n.223G>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 0.462 in 152,144 control chromosomes in the GnomAD database, including 17,181 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 0.46 (17169 hom., cov: 32)
  • Exomes 𝑓: 0.59 (12 hom.)
• Consequence: ENSG00000279593 ENST00000623423.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

ENSG00000279593 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93895984G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279593	ENST00000623423.1	n.223G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70241 AN: 151968 Hom.: 17172 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.0108

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.467

GnomAD4 exome AF: 0.586 AC: 34 AN: 58 Hom.: 12 Cov.: 0 AF XY: 0.625 AC XY: 25 AN XY: 40

Gnomad4 AMR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.596

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.462 AC: 70265 AN: 152086 Hom.: 17169 Cov.: 32 AF XY: 0.455 AC XY: 33797 AN XY: 74310

Gnomad4 AFR AF: 0.484

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.463

Alfa AF: 0.499 Hom.: 29119

Bravo AF: 0.454

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4905110; hg19: chr14-94362330;