chr6-32945469-C-T

Variant names:

• chr6-32945469-C-T
• rs1480380
• ENST00000429234.1:c.89-4654G>A

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248993	ENST00000429234.1	c.89-4654G>A		intron_variant	Intron 1 of 3	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;