chr14-87829256-A-G

Variant names:

• chr14-87829256-A-G
• rs4322600
• ENST00000554305.5:n.111-13005T>C

Variant summary

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

The ENST00000554305.5(ENSG00000258807):​n.111-13005T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,066 control chromosomes in the GnomAD database, including 46,274 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 0.78 (46274 hom., cov: 31)
• Consequence: ENSG00000258807 ENST00000554305.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 16 publications found

Genes affected

ENSG00000258807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 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
ENSG00000258807	ENST00000554305.5	n.111-13005T>C		intron_variant	Intron 2 of 6	5
ENSG00000259077	ENST00000555913.1	n.293-8586A>G		intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118247 AN: 151948 Hom.: 46219 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.778 AC: 118365 AN: 152066 Hom.: 46274 Cov.: 31 AF XY: 0.783 AC XY: 58229 AN XY: 74330

African (AFR) AF: 0.801 AC: 33233 AN: 41466

American (AMR) AF: 0.835 AC: 12753 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2980 AN: 3466

East Asian (EAS) AF: 0.942 AC: 4864 AN: 5162

South Asian (SAS) AF: 0.845 AC: 4067 AN: 4814

European-Finnish (FIN) AF: 0.754 AC: 7982 AN: 10590

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49951 AN: 67982

Other (OTH) AF: 0.773 AC: 1633 AN: 2112

Alfa AF: 0.755 Hom.: 137154

Bravo AF: 0.787

Asia WGS AF: 0.893 AC: 3106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.57
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4322600; hg19: chr14-88295600;