ENST00000554926.1:n.194+10560G>A

Variant names:

• chr14-76715959-C-T
• rs10483877
• ENST00000554926.1:n.194+10560G>A

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.194+10560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,972 control chromosomes in the GnomAD database, including 34,580 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 (34580 hom., cov: 31)
• Consequence: ENSG00000259124 ENST00000554926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.86
• Publications: 21 publications found

Genes affected

ENSG00000259124 (HGNC:):

VASH1-DT (HGNC:55446): (VASH1 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554926.1. 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
	ENSG00000259124	ENST00000554926.1	TSL:3	n.194+10560G>A		intron	N/A
	VASH1-DT	ENST00000556271.1	TSL:3	n.204-4098G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101186 AN: 151854 Hom.: 34575 Cov.: 31

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.666 AC: 101224 AN: 151972 Hom.: 34580 Cov.: 31 AF XY: 0.662 AC XY: 49150 AN XY: 74266

African (AFR) AF: 0.512 AC: 21190 AN: 41424

American (AMR) AF: 0.705 AC: 10763 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2631 AN: 3468

East Asian (EAS) AF: 0.551 AC: 2841 AN: 5156

South Asian (SAS) AF: 0.647 AC: 3105 AN: 4800

European-Finnish (FIN) AF: 0.693 AC: 7321 AN: 10566

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51063 AN: 67974

Other (OTH) AF: 0.682 AC: 1440 AN: 2112

Alfa AF: 0.717 Hom.: 126445

Bravo AF: 0.657

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	15
DANN	Benign	0.62
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs10483877; hg19: chr14-77182302;