rs11721

Variant names:

• chr1-1217251-C-A
• rs11721
• NM_016176.6:c.*261G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-1217251-C-A
• chr1-1217251-C-G
• chr1-1217251-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 23 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016176.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDF4	NM_016176.6	MANE Select	c.*261G>T		3_prime_UTR	Exon 7 of 7	NP_057260.3
	SDF4	NM_016547.3		c.*419G>T		3_prime_UTR	Exon 7 of 7	NP_057631.2	A0A5F9UJX7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDF4	ENST00000360001.12	TSL:1 MANE Select	c.*261G>T		3_prime_UTR	Exon 7 of 7	ENSP00000353094.7	A0A5F9UP49
	SDF4	ENST00000263741.12	TSL:1	c.*419G>T		3_prime_UTR	Exon 7 of 7	ENSP00000263741.8	A0A5F9UJX7
	SDF4	ENST00000900950.1		c.*261G>T		3_prime_UTR	Exon 7 of 7	ENSP00000571009.1

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

African (AFR) AF: 0.214 AC: 120 AN: 562

American (AMR) AF: 0.0750 AC: 54 AN: 720

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 29 AN: 780

East Asian (EAS) AF: 0.257 AC: 557 AN: 2168

South Asian (SAS) AF: 0.0692 AC: 18 AN: 260

European-Finnish (FIN) AF: 0.131 AC: 595 AN: 4554

Middle Eastern (MID) AF: 0.0373 AC: 5 AN: 134

European-Non Finnish (NFE) AF: 0.0795 AC: 1535 AN: 19320

Other (OTH) AF: 0.0987 AC: 168 AN: 1702

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

African (AFR) AF: 0.225 AC: 9329 AN: 41506

American (AMR) AF: 0.0670 AC: 1025 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1287 AN: 5154

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4822

European-Finnish (FIN) AF: 0.125 AC: 1319 AN: 10586

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0859 AC: 5840 AN: 67962

Other (OTH) AF: 0.120 AC: 253 AN: 2104

Alfa AF: 0.104 Hom.: 733

Bravo AF: 0.132

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.89
DANN	Benign	0.69
PhyloP100		-0.46
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: rs11721; hg19: chr1-1152631;