14-23727926-T-G

Variant names:

• chr14-23727926-T-G
• rs12894928
• ENST00000652858.1:n.1669A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652858.1(ENSG00000258464):​n.1669A>C 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 0.496 in 151,986 control chromosomes in the GnomAD database, including 19,296 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 0.50 (19296 hom., cov: 32)
• Consequence: ENSG00000258464 ENST00000652858.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 1 publications found

Genes affected

ENSG00000258464 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652858.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258464	ENST00000652858.1		n.1669A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000258464	ENST00000658193.1		n.148+1652A>C		intron	N/A
	ENSG00000258464	ENST00000660075.1		n.148+1652A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75381 AN: 151868 Hom.: 19294 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.0615

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.496 AC: 75416 AN: 151986 Hom.: 19296 Cov.: 32 AF XY: 0.491 AC XY: 36477 AN XY: 74268

African (AFR) AF: 0.490 AC: 20306 AN: 41440

American (AMR) AF: 0.422 AC: 6440 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2074 AN: 3468

East Asian (EAS) AF: 0.0615 AC: 316 AN: 5142

South Asian (SAS) AF: 0.484 AC: 2328 AN: 4814

European-Finnish (FIN) AF: 0.499 AC: 5280 AN: 10572

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36850 AN: 67952

Other (OTH) AF: 0.491 AC: 1037 AN: 2114

Alfa AF: 0.400 Hom.: 1720

Bravo AF: 0.486

Asia WGS AF: 0.282 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.3
DANN	Benign	0.54
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs12894928; hg19: chr14-24197135;