rs878889

Variant names:

• chr14-56754421-G-A
• rs878889
• ENST00000773249.1:n.405-28434C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-56754421-G-A
• chr14-56754421-G-C
• chr14-56754421-G-T

Variant summary

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

The ENST00000773249.1(ENSG00000259133):​n.405-28434C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,108 control chromosomes in the GnomAD database, including 2,206 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 0.16 (2206 hom., cov: 33)
• Consequence: ENSG00000259133 ENST00000773249.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 9 publications found

Genes affected

ENSG00000259133 (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 (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773249.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259133	ENST00000773249.1		n.405-28434C>T		intron	N/A
	ENSG00000259133	ENST00000773250.1		n.257-28434C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24829 AN: 151992 Hom.: 2196 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.164 AC: 24887 AN: 152108 Hom.: 2206 Cov.: 33 AF XY: 0.161 AC XY: 11990 AN XY: 74366

African (AFR) AF: 0.204 AC: 8474 AN: 41464

American (AMR) AF: 0.215 AC: 3290 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5182

South Asian (SAS) AF: 0.137 AC: 661 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10578

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9606 AN: 67984

Other (OTH) AF: 0.169 AC: 357 AN: 2112

Alfa AF: 0.151 Hom.: 4425

Bravo AF: 0.174

Asia WGS AF: 0.123 AC: 433 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.54
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs878889; hg19: chr14-57221139;