rs13104971

Variant names:

• chr4-52953988-A-G
• rs13104971
• NM_152540.4:c.1562-33118T>C

Variant summary

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

The ENST00000401642.8(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 ENST00000401642.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 2 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]

ENSG00000248115 (HGNC:58243):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000401642.8. 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
	SCFD2	NM_152540.4	MANE Select	c.1562-33118T>C		intron	N/A	NP_689753.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCFD2	ENST00000401642.8	TSL:1 MANE Select	c.1562-33118T>C		intron	N/A	ENSP00000384182.3
	SCFD2	ENST00000388940.8	TSL:2	c.1562-33118T>C		intron	N/A	ENSP00000373592.4
	ENSG00000248115	ENST00000508813.1	TSL:2	n.346-1980A>G		intron	N/A

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

African (AFR) AF: 0.0428 AC: 1777 AN: 41540

American (AMR) AF: 0.108 AC: 1649 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1420 AN: 5152

South Asian (SAS) AF: 0.229 AC: 1107 AN: 4824

European-Finnish (FIN) AF: 0.149 AC: 1574 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8692 AN: 68000

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.109 Hom.: 1098

Bravo AF: 0.0998

Asia WGS AF: 0.245 AC: 851 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.80
PhyloP100		0.18
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: rs13104971; hg19: chr4-53820155;