22-24547326-C-T

Variant summary

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

The NM_001284254.2(GUCD1):c.295-321G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 311,472 control chromosomes in the GnomAD database, including 3,187 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 0.14 (1488 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1699 hom.)
• Consequence: GUCD1 NM_001284254.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

Genes affected

GUCD1 (HGNC:14237): (guanylyl cyclase domain containing 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GUCD1	NM_001284254.2	c.295-321G>A		intron_variant		ENST00000435822.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GUCD1	ENST00000435822.6	c.295-321G>A		intron_variant		1	NM_001284254.2	P3

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20809 AN: 151894 Hom.: 1486 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.136 AC: 21678 AN: 159460 Hom.: 1699 Cov.: 0 AF XY: 0.140 AC XY: 11862 AN XY: 84578

Gnomad4 AFR exome AF: 0.121

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.150

Gnomad4 EAS exome AF: 0.0740

Gnomad4 SAS exome AF: 0.197

Gnomad4 FIN exome AF: 0.120

Gnomad4 NFE exome AF: 0.128

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.137 AC: 20814 AN: 152012 Hom.: 1488 Cov.: 32 AF XY: 0.140 AC XY: 10417 AN XY: 74314

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.137

Alfa AF: 0.136 Hom.: 1957

Bravo AF: 0.136

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.1
Dann	Benign	0.66

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: rs12170895; hg19: chr22-24943294;