rs1889364

Variant names:

• chr14-101497049-A-G
• rs1889364
• ENST00000725604.1:n.90-515A>G

Variant summary

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

The ENST00000725604.1(ENSG00000294743):​n.90-515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,664 control chromosomes in the GnomAD database, including 20,712 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 0.51 (20712 hom., cov: 29)
• Consequence: ENSG00000294743 ENST00000725604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 1 publications found

Genes affected

ENSG00000294743 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000725604.1. 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
	ENSG00000294743	ENST00000725604.1		n.90-515A>G		intron	N/A
	ENSG00000294743	ENST00000725605.1		n.231-515A>G		intron	N/A
	ENSG00000294743	ENST00000725606.1		n.134-515A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77073 AN: 151546 Hom.: 20683 Cov.: 29

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.509 AC: 77145 AN: 151664 Hom.: 20712 Cov.: 29 AF XY: 0.503 AC XY: 37296 AN XY: 74088

African (AFR) AF: 0.686 AC: 28368 AN: 41344

American (AMR) AF: 0.354 AC: 5397 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1885 AN: 5116

South Asian (SAS) AF: 0.484 AC: 2319 AN: 4792

European-Finnish (FIN) AF: 0.424 AC: 4467 AN: 10530

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31631 AN: 67880

Other (OTH) AF: 0.489 AC: 1024 AN: 2094

Alfa AF: 0.481 Hom.: 2841

Bravo AF: 0.508

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.76
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1889364; hg19: chr14-101963386;