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. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000279593 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623423.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279593	ENST00000623423.1	TSL:6	n.223G>A		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.596 AC: 31 AN: 52

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.484 AC: 20090 AN: 41504

American (AMR) AF: 0.358 AC: 5466 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1773 AN: 3468

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5178

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4824

European-Finnish (FIN) AF: 0.472 AC: 4982 AN: 10554

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34818 AN: 67962

Other (OTH) AF: 0.463 AC: 978 AN: 2114

Alfa AF: 0.491 Hom.: 70611

Bravo AF: 0.454

Asia WGS AF: 0.167 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4905110; hg19: chr14-94362330;