4-89514123-C-T

Variant names:

• chr4-89514123-C-T
• rs729685
• ENST00000659714.1:n.546+22629C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659714.1(ENSG00000251095):​n.546+22629C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,978 control chromosomes in the GnomAD database, including 34,441 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 0.67 (34441 hom., cov: 31)
• Consequence: ENSG00000251095 ENST00000659714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

ENSG00000251095 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.795 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
ENSG00000251095	ENST00000659714.1	n.546+22629C>T		intron_variant	Intron 1 of 2
ENSG00000251095	ENST00000659878.1	n.360-73698C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102042 AN: 151860 Hom.: 34409 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.672 AC: 102123 AN: 151978 Hom.: 34441 Cov.: 31 AF XY: 0.671 AC XY: 49791 AN XY: 74252

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.725

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.667

Alfa AF: 0.608 Hom.: 1960

Bravo AF: 0.672

Asia WGS AF: 0.730 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs729685; hg19: chr4-90435274;