14-87702658-A-G

Variant names:

• chr14-87702658-A-G
• rs4899920
• ENST00000556168.2:n.487+23297T>C

Variant summary

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

The ENST00000556168.2(ENSG00000258807):​n.487+23297T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 152,196 control chromosomes in the GnomAD database, including 66,778 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 0.93 (66778 hom., cov: 31)
• Consequence: ENSG00000258807 ENST00000556168.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556168.2. 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
	ENSG00000258807	ENST00000556168.2	TSL:5	n.487+23297T>C		intron	N/A
	ENSG00000295656	ENST00000731587.1		n.205-26395A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142055 AN: 152078 Hom.: 66746 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.993

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.976

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.934 AC: 142142 AN: 152196 Hom.: 66778 Cov.: 31 AF XY: 0.936 AC XY: 69619 AN XY: 74406

African (AFR) AF: 0.819 AC: 33974 AN: 41470

American (AMR) AF: 0.967 AC: 14802 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 3338 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5160 AN: 5160

South Asian (SAS) AF: 0.993 AC: 4793 AN: 4826

European-Finnish (FIN) AF: 0.996 AC: 10566 AN: 10612

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.976 AC: 66404 AN: 68040

Other (OTH) AF: 0.939 AC: 1983 AN: 2112

Alfa AF: 0.967 Hom.: 31047

Bravo AF: 0.926

Asia WGS AF: 0.985 AC: 3425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.065
DANN	Benign	0.31
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4899920; hg19: chr14-88169002;