rs4904864

Variant names:

• chr14-92298175-A-G
• rs4904864
• ENST00000826664.1:n.122-6233A>G

Variant summary

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

The ENST00000826664.1(ENSG00000307514):​n.122-6233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,930 control chromosomes in the GnomAD database, including 23,937 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 0.55 (23937 hom., cov: 31)
• Consequence: ENSG00000307514 ENST00000826664.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 5 publications found

Genes affected

ENSG00000307514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826664.1. 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
	ENSG00000307514	ENST00000826664.1		n.122-6233A>G		intron	N/A
	ENSG00000307514	ENST00000826665.1		n.117-6233A>G		intron	N/A
	ENSG00000307514	ENST00000826666.1		n.113-6233A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83721 AN: 151814 Hom.: 23928 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.551 AC: 83767 AN: 151930 Hom.: 23937 Cov.: 31 AF XY: 0.545 AC XY: 40474 AN XY: 74238

African (AFR) AF: 0.435 AC: 18005 AN: 41398

American (AMR) AF: 0.485 AC: 7414 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2236 AN: 5166

South Asian (SAS) AF: 0.468 AC: 2255 AN: 4820

European-Finnish (FIN) AF: 0.601 AC: 6327 AN: 10528

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43808 AN: 67962

Other (OTH) AF: 0.526 AC: 1105 AN: 2102

Alfa AF: 0.599 Hom.: 20251

Bravo AF: 0.534

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.46
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs4904864; hg19: chr14-92764519;