4-52964590-C-A

Variant names:

• chr4-52964590-C-A
• rs301088
• NM_152540.4:c.1562-43720G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152540.4(SCFD2):​c.1562-43720G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,878 control chromosomes in the GnomAD database, including 20,672 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 0.52 (20672 hom., cov: 32)
• Consequence: SCFD2 NM_152540.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCFD2	NM_152540.4	c.1562-43720G>T		intron_variant	Intron 5 of 8	ENST00000401642.8	NP_689753.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCFD2	ENST00000401642.8	c.1562-43720G>T		intron_variant	Intron 5 of 8	1	NM_152540.4	ENSP00000384182.3
SCFD2	ENST00000388940.8	c.1562-43720G>T		intron_variant	Intron 5 of 7	2		ENSP00000373592.4

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78500 AN: 151764 Hom.: 20659 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.517 AC: 78551 AN: 151878 Hom.: 20672 Cov.: 32 AF XY: 0.519 AC XY: 38503 AN XY: 74210

African (AFR) AF: 0.432 AC: 17891 AN: 41390

American (AMR) AF: 0.635 AC: 9684 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2587 AN: 5164

South Asian (SAS) AF: 0.649 AC: 3118 AN: 4808

European-Finnish (FIN) AF: 0.511 AC: 5371 AN: 10520

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36430 AN: 67958

Other (OTH) AF: 0.509 AC: 1076 AN: 2114

Alfa AF: 0.531 Hom.: 69884

Bravo AF: 0.519

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.5
DANN	Benign	0.65
PhyloP100		-0.055
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: rs301088; hg19: chr4-53830757;