rs1183380347

Variant names:

• chr7-3301849-C-G
• rs1183380347
• NM_152744.4:c.263C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-3301849-C-G
• chr7-3301849-C-A
• chr7-3301849-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_152744.4(SDK1):​c.263C>G​(p.Ala88Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,133,858 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000037 (0 hom.)
• Consequence: SDK1 NM_152744.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.224
• Publications: 2 publications found

Genes affected

SDK1 (HGNC:19307): (sidekick cell adhesion molecule 1) The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]

SDK1-AS1 (HGNC:40883): (SDK1 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.088547766).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152744.4. 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
	SDK1	NM_152744.4	MANE Select	c.263C>G	p.Ala88Gly	missense	Exon 1 of 45	NP_689957.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SDK1	ENST00000404826.7	TSL:1 MANE Select	c.263C>G	p.Ala88Gly	missense	Exon 1 of 45	ENSP00000385899.2	Q7Z5N4-1
	SDK1	ENST00000389531.7	TSL:5	c.263C>G	p.Ala88Gly	missense	Exon 1 of 44	ENSP00000374182.3	F8W6X9
	SDK1-AS1	ENST00000437354.2	TSL:3	n.224+380G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000133 AC: 2 AN: 149992 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000297

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000366 AC: 36 AN: 983762 Hom.: 0 Cov.: 32 AF XY: 0.0000389 AC XY: 18 AN XY: 463276

African (AFR) AF: 0.000358 AC: 7 AN: 19570

American (AMR) AF: 0.00 AC: 0 AN: 5192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10280

East Asian (EAS) AF: 0.00 AC: 0 AN: 17840

South Asian (SAS) AF: 0.00 AC: 0 AN: 18720

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 14412

Middle Eastern (MID) AF: 0.000410 AC: 1 AN: 2438

European-Non Finnish (NFE) AF: 0.0000303 AC: 26 AN: 858646

Other (OTH) AF: 0.0000545 AC: 2 AN: 36664

GnomAD4 genome AF: 0.0000133 AC: 2 AN: 150096 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 73288

African (AFR) AF: 0.00 AC: 0 AN: 41280

American (AMR) AF: 0.00 AC: 0 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3440

East Asian (EAS) AF: 0.00 AC: 0 AN: 5064

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9732

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000297 AC: 2 AN: 67378

Other (OTH) AF: 0.00 AC: 0 AN: 2078

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000264

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Benign	0.36
DEOGEN2	Benign	0.035	T
Eigen	Benign	-0.94
Eigen_PC	Benign	-0.91
FATHMM_MKL	Benign	0.19	N
LIST_S2	Benign	0.43	T
M_CAP	Uncertain	0.20	D
MetaRNN	Benign	0.089	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.22
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-0.32	N
REVEL	Benign	0.043
Sift	Benign	0.49	T
Sift4G	Benign	0.14	T
Polyphen		0.013	B
Vest4		0.076
MutPred		0.46		Loss of stability (P = 0.0698)
MVP		0.20
MPC		0.069
ClinPred		0.021	T
GERP RS		-1.0
PromoterAI		0.011	Neutral
Varity_R		0.038
gMVP		0.25
Mutation Taster		=95/5	polymorphism

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: rs1183380347; hg19: chr7-3341481;