9-133461126-T-G

Position:

• chr9-133461126-T-G

Variant summary

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

The NM_017586.5(CACFD1):​c.121+939T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,268 control chromosomes in the GnomAD database, including 49,181 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 0.80 (49181 hom., cov: 34)
• Consequence: CACFD1 NM_017586.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

Genes affected

CACFD1 (HGNC:1365): (calcium channel flower domain containing 1) Predicted to be involved in vesicle-mediated transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

CACFD1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACFD1	NM_017586.5	c.121+939T>G		intron_variant		ENST00000316948.9	NP_060056.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACFD1	ENST00000316948.9	c.121+939T>G		intron_variant		1	NM_017586.5	ENSP00000317121.4

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121538 AN: 152150 Hom.: 49130 Cov.: 34

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.799 AC: 121648 AN: 152268 Hom.: 49181 Cov.: 34 AF XY: 0.802 AC XY: 59746 AN XY: 74476

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.851

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.808

Alfa AF: 0.793 Hom.: 3635

Bravo AF: 0.793

Asia WGS AF: 0.885 AC: 3076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.72

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: rs739468; hg19: chr9-136326248;