chr14-30727754-C-G

Variant names:

• chr14-30727754-C-G
• rs9322864
• NM_016106.4:c.1836+5195C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016106.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCFD1	NM_016106.4	MANE Select	c.1836+5195C>G		intron	N/A	NP_057190.2
	SCFD1	NM_001283032.1		c.1659+5195C>G		intron	N/A	NP_001269961.1
	SCFD1	NM_182835.2		c.1635+5195C>G		intron	N/A	NP_878255.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCFD1	ENST00000458591.7	TSL:1 MANE Select	c.1836+5195C>G		intron	N/A	ENSP00000390783.2
	SCFD1	ENST00000556768.5	TSL:1	n.*1306+5195C>G		intron	N/A	ENSP00000451811.1
	SCFD1	ENST00000676509.1		c.1833+5195C>G		intron	N/A	ENSP00000504739.1

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

African (AFR) AF: 0.624 AC: 25851 AN: 41420

American (AMR) AF: 0.417 AC: 6369 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1147 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3241 AN: 5172

South Asian (SAS) AF: 0.349 AC: 1678 AN: 4814

European-Finnish (FIN) AF: 0.306 AC: 3227 AN: 10558

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20271 AN: 67960

Other (OTH) AF: 0.405 AC: 856 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		0.090
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9322864; hg19: chr14-31196960;