rs1480380

Positions:

• chr6-32945469-C-T

Variant summary

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

The ENST00000429234.1(ENSG00000248993):​c.89-4654G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,110 control chromosomes in the GnomAD database, including 1,033 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 0.10 (1033 hom., cov: 31)
• Consequence: ENSG00000248993 ENST00000429234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191

Genes affected

ENSG00000248993 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32945469C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000248993	ENST00000429234.1	c.89-4654G>A		intron_variant		2		ENSP00000412457.1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15948 AN: 151992 Hom.: 1034 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0584

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.00806

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.105 AC: 15965 AN: 152110 Hom.: 1033 Cov.: 31 AF XY: 0.0991 AC XY: 7368 AN XY: 74380

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0729

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.00808

Gnomad4 SAS AF: 0.0114

Gnomad4 FIN AF: 0.0605

Gnomad4 NFE AF: 0.0887

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0838 Hom.: 858

Bravo AF: 0.112

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1480380; hg19: chr6-32913246;