rs1029440073

Variant names:

• chr7-3301788-T-G
• rs1029440073
• NM_152744.4:c.202T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-3301788-T-G
• chr7-3301788-T-A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_152744.4(SDK1):​c.202T>G​(p.Cys68Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000218 in 1,010,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 31)
  • Exomes 𝑓: 0.0000069 (0 hom.)
• Consequence: SDK1 NM_152744.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.994
• Publications: 0 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.050824463).

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.202T>G	p.Cys68Gly	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.202T>G	p.Cys68Gly	missense	Exon 1 of 45	ENSP00000385899.2	Q7Z5N4-1
	SDK1	ENST00000389531.7	TSL:5	c.202T>G	p.Cys68Gly	missense	Exon 1 of 44	ENSP00000374182.3	F8W6X9
	SDK1-AS1	ENST00000437354.2	TSL:3	n.224+441A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000112 AC: 16 AN: 142470 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000380

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: 0.0000156

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000691 AC: 6 AN: 868186 Hom.: 0 Cov.: 31 AF XY: 0.00000495 AC XY: 2 AN XY: 404116

African (AFR) AF: 0.00 AC: 0 AN: 16520

American (AMR) AF: 0.00 AC: 0 AN: 2156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6062

East Asian (EAS) AF: 0.00 AC: 0 AN: 5616

South Asian (SAS) AF: 0.00 AC: 0 AN: 17578

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4184

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1784

European-Non Finnish (NFE) AF: 0.00000765 AC: 6 AN: 784792

Other (OTH) AF: 0.00 AC: 0 AN: 29494

GnomAD4 genome AF: 0.000112 AC: 16 AN: 142470 Hom.: 0 Cov.: 31 AF XY: 0.000144 AC XY: 10 AN XY: 69370

African (AFR) AF: 0.000380 AC: 15 AN: 39518

American (AMR) AF: 0.00 AC: 0 AN: 14542

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3330

East Asian (EAS) AF: 0.00 AC: 0 AN: 4740

South Asian (SAS) AF: 0.00 AC: 0 AN: 4586

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8322

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 280

European-Non Finnish (NFE) AF: 0.0000156 AC: 1 AN: 64294

Other (OTH) AF: 0.00 AC: 0 AN: 1996

Alfa AF: 0.00 Hom.: 0

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	0.043
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.0
DANN	Benign	0.25
DEOGEN2	Benign	0.025	T
Eigen	Benign	-1.7
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.024	N
LIST_S2	Benign	0.24	T
M_CAP	Benign	0.051	D
MetaRNN	Benign	0.051	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.0	N
PhyloP100		-0.99
PrimateAI	Uncertain	0.63	T
PROVEAN	Benign	-0.060	N
REVEL	Benign	0.053
Sift	Benign	0.52	T
Polyphen		0.0	B
Vest4		0.18
MutPred		0.47		Loss of helix (P = 0.0076)
MVP		0.076
MPC		0.10
ClinPred		0.036	T
GERP RS		-3.9
PromoterAI		0.078	Neutral
Varity_R		0.048
gMVP		0.093
Mutation Taster		=96/4	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: rs1029440073; hg19: chr7-3341420;