chr9-133461126-T-G

Variant names:

• chr9-133461126-T-G
• rs739468
• NM_017586.5:c.121+939T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017586.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACFD1	NM_017586.5	MANE Select	c.121+939T>G		intron	N/A	NP_060056.1
	CACFD1	NM_001242369.2		c.121+939T>G		intron	N/A	NP_001229298.1
	CACFD1	NM_001242370.2		c.121+939T>G		intron	N/A	NP_001229299.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACFD1	ENST00000316948.9	TSL:1 MANE Select	c.121+939T>G		intron	N/A	ENSP00000317121.4
	CACFD1	ENST00000540581.5	TSL:2	c.121+939T>G		intron	N/A	ENSP00000440832.1
	CACFD1	ENST00000542192.5	TSL:2	c.121+939T>G		intron	N/A	ENSP00000444328.1

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

African (AFR) AF: 0.672 AC: 27899 AN: 41520

American (AMR) AF: 0.851 AC: 13026 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2564 AN: 3472

East Asian (EAS) AF: 0.927 AC: 4804 AN: 5182

South Asian (SAS) AF: 0.873 AC: 4216 AN: 4828

European-Finnish (FIN) AF: 0.828 AC: 8791 AN: 10616

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57835 AN: 68020

Other (OTH) AF: 0.808 AC: 1709 AN: 2116

Alfa AF: 0.785 Hom.: 3816

Bravo AF: 0.793

Asia WGS AF: 0.885 AC: 3076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.72
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs739468; hg19: chr9-136326248;