rs2887286

Positions:

• chr1-1220751-T-C

Variant summary

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

The NM_016176.6(SDF4):​c.557-1824A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,288,494 control chromosomes in the GnomAD database, including 46,944 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 0.31 (10080 hom., cov: 34)
  • Exomes 𝑓: 0.22 (36864 hom.)
• Consequence: SDF4 NM_016176.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470

Genes affected

SDF4 (HGNC:24188): (stromal cell derived factor 4) This gene encodes a stromal cell derived factor that is a member of the CREC protein family. The encoded protein contains six EF-hand motifs and calcium-binding motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDF4	NM_016176.6	c.557-1824A>G		intron_variant		ENST00000360001.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDF4	ENST00000360001.12	c.557-1824A>G		intron_variant		1	NM_016176.6	P1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47478 AN: 151878 Hom.: 10048 Cov.: 34

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.300

GnomAD3 exomes AF: 0.368 AC: 47149 AN: 128100 Hom.: 12049 AF XY: 0.366 AC XY: 25679 AN XY: 70134

Gnomad AFR exome AF: 0.486

Gnomad AMR exome AF: 0.539

Gnomad ASJ exome AF: 0.162

Gnomad EAS exome AF: 0.844

Gnomad SAS exome AF: 0.505

Gnomad FIN exome AF: 0.171

Gnomad NFE exome AF: 0.161

Gnomad OTH exome AF: 0.276

GnomAD4 exome AF: 0.217 AC: 246972 AN: 1136498 Hom.: 36864 Cov.: 35 AF XY: 0.226 AC XY: 125990 AN XY: 557538

Gnomad4 AFR exome AF: 0.479

Gnomad4 AMR exome AF: 0.535

Gnomad4 ASJ exome AF: 0.161

Gnomad4 EAS exome AF: 0.839

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.175

Gnomad4 NFE exome AF: 0.168

Gnomad4 OTH exome AF: 0.262

GnomAD4 genome AF: 0.313 AC: 47559 AN: 151996 Hom.: 10080 Cov.: 34 AF XY: 0.321 AC XY: 23823 AN XY: 74304

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.835

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.307

Alfa AF: 0.203 Hom.: 6195

Bravo AF: 0.336

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs2887286; hg19: chr1-1156131;