rs9322864

chr14-30727754-C-Gchr14-30727754-C-T

Variant summary

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

The NM_016106.4(SCFD1):c.1836+5195C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,992 control chromosomes in the GnomAD database, including 14,733 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 0.42 (14733 hom., cov: 32)
• Consequence: SCFD1 NM_016106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

SCFD1 (HGNC:20726): (sec1 family domain containing 1) Predicted to enable syntaxin binding activity. Involved in negative regulation of autophagosome assembly; regulation of protein transport; and response to toxic substance. Located in cis-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCFD1	NM_016106.4	c.1836+5195C>G		intron_variant		ENST00000458591.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCFD1	ENST00000458591.7	c.1836+5195C>G		intron_variant		1	NM_016106.4	A2

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63204 AN: 151874 Hom.: 14717 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.416 AC: 63265 AN: 151992 Hom.: 14733 Cov.: 32 AF XY: 0.418 AC XY: 31021 AN XY: 74294

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.405

Alfa AF: 0.357 Hom.: 1333

Bravo AF: 0.439

Asia WGS AF: 0.486 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9322864; hg19: chr14-31196960;