14-23727926-T-G

Position:

• chr14-23727926-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000258464 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370409	XR_001750657.2	n.328+1351A>C		intron_variant
LOC105370409	XR_002957608.2	n.313+1351A>C		intron_variant
LOC105370409	XR_007064080.1	n.165+1652A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258464	ENST00000652858.1	n.1669A>C		non_coding_transcript_exon_variant	2/2
ENSG00000258464	ENST00000658193.1	n.148+1652A>C		intron_variant
ENSG00000258464	ENST00000660075.1	n.148+1652A>C		intron_variant

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

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.0615

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.491

Alfa AF: 0.395 Hom.: 1614

Bravo AF: 0.486

Asia WGS AF: 0.282 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12894928; hg19: chr14-24197135;