4-52953988-A-G

Position:

• chr4-52953988-A-G

Variant summary

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

The NM_152540.4(SCFD2):​c.1562-33118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,182 control chromosomes in the GnomAD database, including 1,178 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 0.11 (1178 hom., cov: 32)
• Consequence: SCFD2 NM_152540.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

SCFD2 (HGNC:30676): (sec1 family domain containing 2) Predicted to enable syntaxin binding activity. Predicted to be involved in intracellular protein transport and vesicle docking involved in exocytosis. Predicted to be active in plasma membrane and secretory granule. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCFD2	NM_152540.4	c.1562-33118T>C		intron_variant		ENST00000401642.8	NP_689753.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCFD2	ENST00000401642.8	c.1562-33118T>C		intron_variant		1	NM_152540.4	ENSP00000384182	P1
	ENST00000508813.1	n.346-1980A>G		intron_variant, non_coding_transcript_variant		2
SCFD2	ENST00000388940.8	c.1562-33118T>C		intron_variant		2		ENSP00000373592

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16715 AN: 152064 Hom.: 1176 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.110 AC: 16728 AN: 152182 Hom.: 1178 Cov.: 32 AF XY: 0.113 AC XY: 8402 AN XY: 74410

Gnomad4 AFR AF: 0.0428

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0643

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0936

Alfa AF: 0.113 Hom.: 921

Bravo AF: 0.0998

Asia WGS AF: 0.245 AC: 851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.80

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: rs13104971; hg19: chr4-53820155;