rs10483877

Positions:

• chr14-76715959-C-T

Variant summary

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

The ENST00000554926.1(ENSG00000259124):​n.194+10560G>A variant causes a intron, non coding transcript 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: ENST00000554926.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.86

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370577	XR_007064273.1	n.194-5144G>A		intron_variant, non_coding_transcript_variant
LOC105370577	XR_001750834.2	n.415+2627G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000554926.1	n.194+10560G>A		intron_variant, non_coding_transcript_variant		3
VASH1-DT	ENST00000556271.1	n.204-4098G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.682

Alfa AF: 0.731 Hom.: 55188

Bravo AF: 0.657

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483877; hg19: chr14-77182302;