rs4899554

Variant names:

• chr14-75234518-C-T
• rs4899554
• ENST00000789955.1:n.127-23513G>A

Variant summary

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

The ENST00000789955.1(ENSG00000258740):​n.127-23513G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,972 control chromosomes in the GnomAD database, including 1,857 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 0.14 (1857 hom., cov: 31)
• Consequence: ENSG00000258740 ENST00000789955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 34 publications found

Genes affected

ENSG00000258740 (HGNC:58290):

ENSG00000302861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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
ENSG00000258740	ENST00000789955.1	n.127-23513G>A		intron_variant	Intron 1 of 1
ENSG00000258740	ENST00000789956.1	n.136-1757G>A		intron_variant	Intron 1 of 1
ENSG00000302861	ENST00000790105.1	n.409-2432C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21681 AN: 151854 Hom.: 1846 Cov.: 31

Gnomad AFR AF: 0.0549

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.143 AC: 21710 AN: 151972 Hom.: 1857 Cov.: 31 AF XY: 0.141 AC XY: 10485 AN XY: 74258

African (AFR) AF: 0.0550 AC: 2281 AN: 41458

American (AMR) AF: 0.162 AC: 2473 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3472

East Asian (EAS) AF: 0.185 AC: 948 AN: 5136

South Asian (SAS) AF: 0.132 AC: 636 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1761 AN: 10554

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12732 AN: 67944

Other (OTH) AF: 0.135 AC: 286 AN: 2112

Alfa AF: 0.173 Hom.: 4989

Bravo AF: 0.140

Asia WGS AF: 0.154 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4899554; hg19: chr14-75701221;