rs4905110

Variant names:

• chr14-93895984-G-A
• rs4905110
• ENST00000623423.1:n.223G>A

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279593	ENST00000623423.1	n.223G>A		non_coding_transcript_exon_variant	Exon 1 of 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;