chr1-1222897-G-A

Variant names:

• chr1-1222897-G-A
• rs3813199
• NM_016176.6:c.556+347C>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.556+347C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,272 control chromosomes in the GnomAD database, including 1,148 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 (1148 hom., cov: 34)
• Consequence: SDF4 NM_016176.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 24 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 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.556+347C>T		intron	N/A	NP_057260.3
	SDF4	NM_016547.3		c.556+347C>T		intron	N/A	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.556+347C>T		intron	N/A	ENSP00000353094.7	A0A5F9UP49
	SDF4	ENST00000263741.12	TSL:1	c.556+347C>T		intron	N/A	ENSP00000263741.8	A0A5F9UJX7
	SDF4	ENST00000900950.1		c.556+347C>T		intron	N/A	ENSP00000571009.1

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17444 AN: 152154 Hom.: 1142 Cov.: 34

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0934

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.115 AC: 17454 AN: 152272 Hom.: 1148 Cov.: 34 AF XY: 0.116 AC XY: 8620 AN XY: 74460

African (AFR) AF: 0.168 AC: 6969 AN: 41522

American (AMR) AF: 0.0691 AC: 1058 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.175 AC: 906 AN: 5186

South Asian (SAS) AF: 0.0948 AC: 458 AN: 4832

European-Finnish (FIN) AF: 0.0934 AC: 991 AN: 10608

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6471 AN: 68026

Other (OTH) AF: 0.102 AC: 215 AN: 2116

Alfa AF: 0.0996 Hom.: 2942

Bravo AF: 0.117

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.84
PhyloP100		-3.1
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: rs3813199; hg19: chr1-1158277;