chr1-1217251-C-A

Position:

• chr1-1217251-C-A

Variant summary

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

The NM_016176.6(SDF4):​c.*261G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 182,308 control chromosomes in the GnomAD database, including 1,887 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 0.13 (1654 hom., cov: 33)
  • Exomes 𝑓: 0.10 (233 hom.)
• Consequence: SDF4 NM_016176.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDF4	NM_016176.6	c.*261G>T		3_prime_UTR_variant	7/7	ENST00000360001.12
SDF4	NM_016547.3	c.*419G>T		3_prime_UTR_variant	7/7
SDF4	XM_047422111.1	c.*261G>T		3_prime_UTR_variant	7/7
SDF4	XM_047422112.1	c.*419G>T		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDF4	ENST00000360001.12	c.*261G>T		3_prime_UTR_variant	7/7	1	NM_016176.6	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19710 AN: 151990 Hom.: 1635 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0672

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.121

GnomAD4 exome AF: 0.102 AC: 3081 AN: 30200 Hom.: 233 Cov.: 2 AF XY: 0.0997 AC XY: 1588 AN XY: 15922

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.0750

Gnomad4 ASJ exome AF: 0.0372

Gnomad4 EAS exome AF: 0.257

Gnomad4 SAS exome AF: 0.0692

Gnomad4 FIN exome AF: 0.131

Gnomad4 NFE exome AF: 0.0795

Gnomad4 OTH exome AF: 0.0987

GnomAD4 genome AF: 0.130 AC: 19755 AN: 152108 Hom.: 1654 Cov.: 33 AF XY: 0.131 AC XY: 9765 AN XY: 74358

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0670

Gnomad4 ASJ AF: 0.0545

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.0844

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0998 Hom.: 449

Bravo AF: 0.132

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.89
DANN	Benign	0.69

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: rs11721; hg19: chr1-1152631;